The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.

[1]  J. Spouge,et al.  CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms , 2012, PLoS biology.

[2]  Purificación López-García,et al.  The molecular ecology of microbial eukaryotes unveils a hidden world. , 2002, Trends in microbiology.

[3]  J. Avise,et al.  On the temporal inconsistencies of Linnean taxonomic ranks , 2011 .

[4]  Sp Lapage,et al.  International Code of Nomenclature of Bacteria: Bacteriological Code, 1990 Revision , 1992 .

[5]  Wolfgang Ludwig,et al.  Road map of the phyla Bacteroidetes , Spirochaetes , Tenericutes ( Mollicutes ), Acidobacteria , Fibrobacteres , Fusobacteria , Dictyoglomi , Gemmatimonadetes , Lentisphaerae , Verrucomicrobia , Chlamydiae , and Planctomycetes , 2015 .

[6]  Daniel J. G. Lahr,et al.  Time to regulate microbial eukaryote nomenclature , 2012 .

[7]  D. Caron,et al.  Protists are microbes too: a perspective , 2009, The ISME Journal.

[8]  Eric P. Nawrocki,et al.  An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.

[9]  Jang-Cheon Cho,et al.  Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic Time‐series Study site , 2005 .

[10]  J. Gilbert,et al.  Microbial metagenomics: beyond the genome. , 2011, Annual review of marine science.

[11]  K. Schleifer,et al.  The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. , 2008, Systematic and applied microbiology.

[12]  D. Patterson,et al.  The Diversity of Eukaryotes , 1999, The American Naturalist.

[13]  W. Ludwig,et al.  SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB , 2007, Nucleic acids research.

[14]  James R. Cole,et al.  The Ribosomal Database Project: improved alignments and new tools for rRNA analysis , 2008, Nucleic Acids Res..

[15]  David A. Caron,et al.  New Accomplishments and Approaches for Assessing Protistan Diversity and Ecology in Natural Ecosystems , 2009 .

[16]  N. Ryan.  International Code of Nomenclature of Bacteria. Bacteriological Code , 1977 .

[17]  Matthew W. Brown,et al.  The Revised Classification of Eukaryotes , 2012, The Journal of eukaryotic microbiology.

[18]  J. Euzéby.  List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. , 1997, International journal of systematic bacteriology.

[19]  Stéphane Audic,et al.  The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy , 2012, Nucleic Acids Res..

[20]  Scott Federhen,et al.  The NCBI Taxonomy database , 2011, Nucleic Acids Res..

[21]  Aidan C. Parte,et al.  LPSN—list of prokaryotic names with standing in nomenclature , 2013, Nucleic Acids Res..

[22]  G. Garrity.  Bergey’s Manual® of Systematic Bacteriology , 2012, Springer New York.

[23]  Katja Meuser,et al.  Novel lineages of Planctomycetes densely colonize the alkaline gut of soil-feeding termites (Cubitermes spp.). , 2008, Environmental microbiology.

[24]  Andrew McDowell,et al.  Order XII Propionibacteriales ord. nov. , 2012 .

[25]  Raul Munoz,et al.  Release LTPs104 of the All-Species Living Tree. , 2011, Systematic and applied microbiology.

[26]  Laura Wegener Parfrey,et al.  Evaluating Support for the Current Classification of Eukaryotic Diversity , 2006, PLoS genetics.

[27]  W. Whitman,et al.  Prokaryotes: the unseen majority. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[28]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[29]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[30]  Sp Lapage,et al.  International Code of Nomenclature of Bacteria , 1992 .

[31]  George M. Garrity,et al.  The Archaea and the deeply branching and phototrophic bacteria , 2001 .

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

[33]  Ken Takai,et al.  Archaeal Diversity in Waters from Deep South African Gold Mines , 2001, Applied and Environmental Microbiology.

[34]  N. Pace.  A molecular view of microbial diversity and the biosphere. , 1997, Science.

[35]  David Bass,et al.  Diversity , Nomenclature , and Taxonomy of Protists , 2006 .

[36]  S. Adl,et al.  The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists , 2005, The Journal of eukaryotic microbiology.