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.