A taxonomic nomenclature is a set of taxon names and a hierarchy which specifies the sub-taxa belonging to each higher taxon. The hierarchy can be represented as a tree.
At least three prokaryotic taxonomy nomenclatures are widely used. LPT and SILVA are based on Bergey's Manual and LSPN, the Greengenes nomenclature is based on the NCBI Taxonomy database, and RDP uses Bergey's Manual.
If a taxon is defined by traits, then all nomenclatures implicitly agree on the traits. In other words, a taxon name such as Salmonella should, and does, mean the same thing in all nomenclatures where it appears. However, if a taxon name is defined as a group of lower taxa, there may be disagreements on which taxa are included due to the difficulty of inferring phylogenetic relationships from sequence.
As an example of a conflict between taxonomy and sequence, Escherichia and Shigella are overlapping genera according to analysis of genome sequences for their type strains, i.e. these genera are polyphyletic. Greengenes resolves this issue by deleting Escherichia and Shigella, leaving their sequences unclassified at ranks below family Enterobacteriaceae. SILVA, RDP and LTP deal with this issue differently by retaining well-established species names such as Escherichia coli and introducing a combined genus named Escherichia-Shigella.
An example of an environmental candidate group is
Atribacteria (OP9/JS1), which has been adopted in the SILVA
nomenclature but not by RDP or Greengenes at the time of writing.