2014, Vol. 42, Database issue | Pelin Yilmaz, Laura Wegener Parfrey, Pablo Yarza, Jan Gerken, Elmar Pruesse, Christian Quast, Timmy Schweer, Jörg Peplies, Wolfgang Ludwig and Frank Oliver Glöckner
The article discusses the SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks, which are comprehensive resources for quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from Bacteria, Archaea, and Eukaryota. SILVA provides a manually curated taxonomy based on phylogenetic trees for small- and large-subunit rRNA genes. The article highlights improvements in the SILVA taxonomy over the last 3 years, focusing on the curation process, resources used, and comparisons with other taxonomies like Greengenes and RDP-II. It emphasizes the importance of a taxonomic framework for microbiology, noting that most life on Earth is microbial, and that sequence-based methods have significantly increased our understanding of microbial diversity. The article also details the nomenclature and classification of Bacteria, Archaea, and Eukaryota within SILVA, including the use of phylogenetic trees and the inclusion of environmental sequences. Additionally, it compares the SILVA taxonomy with those of RDP-II and Greengenes, highlighting differences in taxonomic names and numbers. The article concludes with an outlook on future developments, including the maintenance of taxonomies, reconciliation of classifications, and the development of the SILVA-NGS pipeline for rRNA gene amplicon data classification.The article discusses the SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks, which are comprehensive resources for quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from Bacteria, Archaea, and Eukaryota. SILVA provides a manually curated taxonomy based on phylogenetic trees for small- and large-subunit rRNA genes. The article highlights improvements in the SILVA taxonomy over the last 3 years, focusing on the curation process, resources used, and comparisons with other taxonomies like Greengenes and RDP-II. It emphasizes the importance of a taxonomic framework for microbiology, noting that most life on Earth is microbial, and that sequence-based methods have significantly increased our understanding of microbial diversity. The article also details the nomenclature and classification of Bacteria, Archaea, and Eukaryota within SILVA, including the use of phylogenetic trees and the inclusion of environmental sequences. Additionally, it compares the SILVA taxonomy with those of RDP-II and Greengenes, highlighting differences in taxonomic names and numbers. The article concludes with an outlook on future developments, including the maintenance of taxonomies, reconciliation of classifications, and the development of the SILVA-NGS pipeline for rRNA gene amplicon data classification.