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The SILVA Taxonomy

In the SILVA taxonomic framework, taxa names are adapted from widely accepted sources, and discrepancies are resolved with the overall aim of making taxonomy consistent with phylogeny. The bacterial and archaeal classification in SILVA is based on Bergey’s Taxonomic Outlines (Boone et al. 2001; Brenner et al. 2005; Vos et al. 2009; Krieg et al. 2010). Since both taxonomy and species are dynamic entities, changes are rapid and supplemental resources are required to stay up-to-date. In such cases, name changes and taxonomic outlines are adapted from the “List of Prokaryotic Names with Standing in Nomenclature” (LPSN) (Euzeby 1997). Moreover, the LPSN resource is also used to track down names without standing in nomenclature (not validly published taxa) and Candidatus taxa.

SILVA taxonomy employs a phylogeny-based process using guide trees, whereas LPSN and Bergey’s classifications are not directly phylogeny-based. Thus, topological differences between the SILVA Ref (NR 99) trees and other resources have to be expected.

In addition to this traditional taxonomic backbone, extensive effort is spent for every release to represent prominent clades known only from environmental sequences. Most of these clades and groups are annotated in the guide tree based on literature surveys and occasionally based on personal communications; therefore, not all clades are available in publications. We chose to name phylogenetically coherent groups above the family rank, consisting only of sequences from uncultured organisms, based on the clone name of the earliest submitted sequence.

Additionally, every sequence in the SILVA datasets carries the EMBL taxonomy assignment. Where available, the greengenes (DeSantis et al. 2006) and RDP (Cole et al. 2014) taxonomies are added for comparison.

References

Boone DR, Castenholz RW, Garrity GM, Staley JT (2001) The Archaea and the Deeply Branching and Phototrophic Bacteria. Opens external link in new windowIn. Springer, New York

Brenner DJ, Krieg NR, Garrity GM, Staley JT (2005) The Proteobacteria. Opens external link in new windowSpringer, New York

Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM (2014) Ribosomal Database Project: data and tools for high throughput rRNA analysis. Opens external link in new windowNucleic Acid Res. 42:D633-D642

DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Opens external link in new windowAppl. Environ. Microbiol. 72:5069-5072

Euzeby JP (1997) List of bacterial names with standing in nomenclature: A folder available on the Internet. Opens external link in new windowInt. J. Syst. Bacteriol. 47:590-592 

Further Reading

Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO (2014) The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Opens external link in new windowNucl. Acids Res. 42:D643-D648

Glöckner FO, Yilmaz P, Quast C, Gerken J, Beccati A, Ciuprina A, Bruns G, Yarza P, Peplies J, Westram R, Ludwig W (2017) 25 years of serving the community with ribosomal RNA gene reference databases and tools. Opens external link in new windowJ. Biotechnol. 261:169