Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses

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 Amann, 1995, Phylogenetic identification and in situ detection of individual microbial cells without cultivation, Microbiol. Rev., 59, 143, 10.1128/MMBR.59.1.143-169.1995 Clayton, 1995, Intraspecific variation in small-subunit rRNA sequences in genbank: why single sequences may not adequately represent prokaryotic taxa, Int. J. Syst. Bacteriol., 45, 595, 10.1099/00207713-45-3-595 Cole, 2009, The Ribosomal Database Project: improved alignments and new tools for rRNA analysis, Nucleic Acids Res., 37, D141, 10.1093/nar/gkn879 Dawyndt, 2005, Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources, IEEE Trans. Knowl. Data Eng., 17, 1111, 10.1109/TKDE.2005.131 Euzéby, 1997, List of bacterial names with standing in nomenclature: a folder available on the Internet, Int. J. Syst. Bacteriol., 47, 590, 10.1099/00207713-47-2-590 Fox, 1977, Comparative cataloguing of 16S ribosomal ribonucleic acid: molecular approach to prokaryotic systematics, Int. J. Bacteriol., 27, 44, 10.1099/00207713-27-1-44 Garrity, 2001 Geissinger, 2009, The ultramicrobacterium “Elusimicrobium minutum” gen. nov., sp. nov., the first cultivated representative of the termite group 1 phylum, Appl. Environ. Microbiol., 75, 2831, 10.1128/AEM.02697-08 Klappenbach, 2001, rrnDB: the ribosomal RNA operon copy number database, Nucleic Acids Res., 29, 181, 10.1093/nar/29.1.181 Kulikova, 2007, EMBL nucleotide sequence database in 2006, Nucleic Acids Res., 35, D16, 10.1093/nar/gkl913 Lapage, 1992, International Code of Nomenclature of Bacteria (1990 Revision) Lee, 2009, rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea, Nucleic Acids Res., 37, D489, 10.1093/nar/gkn689 Liolios, 2008, The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata, Nucleic Acids Res., 36, D475, 10.1093/nar/gkm884 Ludwig, 2010, Molecular Phylogeny of Microorganisms: Is rRNA still a useful marker? Ludwig, 2009, Revised road map to the phylum Firmicutes, vol. 3, 1 Ludwig, 2004, ARB: a software environment for sequence data, Nucleic Acids Res., 32, 1363, 10.1093/nar/gkh293 Ludwig, 2001, Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics, 49 Mylvaganam, 1992, Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui, Genetics, 130, 399, 10.1093/genetics/130.3.399 Mori, 2009, Int. J. Syst. Evol. Microbiol., 53, 2894, 10.1099/ijs.0.010033-0 Olsen, 1986, Microbial ecology and evolution: a ribosomal RNA approach, Annu. Rev. Microbiol., 40, 337, 10.1146/annurev.mi.40.100186.002005 Peplies, 2008, A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes, Syst. Appl. Microbiol., 31, 251, 10.1016/j.syapm.2008.08.003 Pruesse, 2007, SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Res., 35, 7188, 10.1093/nar/gkm864 Richter, 2009, Shifting the genomic gold standard for the prokaryotic species definition, Proc. Natl. Acad. Sci. U.S.A., 106, 19126, 10.1073/pnas.0906412106 Rosselló-Móra, 2001, The species concept for prokaryotes, FEMS Microbiol. Rev., 25, 39, 10.1016/S0168-6445(00)00040-1 Stackebrandt, 2006, Taxonomic parameters revisited: tarnished gold standards, Microbiol. Today, 33, 152 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, 10.1099/ijs.0.02360-0 Stamatakis, 2006, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 22, 2688, 10.1093/bioinformatics/btl446 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 Westram, R., Bader, K., Prüsse, E., Kumar, Y., Meier, H., Glöckner, F.O., Ludwig, W. (2010) ARB: a software environment for sequence data. In: F.J. de Bruijn (Ed.), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. John Wiley & Sons, Hoboken, New Jersey. In press. Wu, 2009, A phylogeny-driven genomic encyclopedia of Bacteria and Archaea, Nature, 462, 1056, 10.1038/nature08656 Yarza, 2008, The All-Species Living Tree Project: a 16S rRNA-based phylogenetic tree of all sequenced type strains, Syst. Appl. Microbiol., 31, 241, 10.1016/j.syapm.2008.07.001 Zhang, 2003, Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov, Int. J. Syst. Evol. Microbiol., 53, 1155, 10.1099/ijs.0.02520-0