Type strains

General remarks

Type strains are of huge relevance for Prokaryotic nomenclature because the serve as nomenclatural types of species and subspecies.

Representation

Subtle differences exist between the presentation of type strains in distinct databases. The two major approaches are best illustrated by an example.
Version 1: The type strain of Geodermatophilus sabuli Hezbri et al. 2015 is BMG 8133, which is represented by DSM 46844 and CECT 8820.
Version 2: The type strain of Geodermatophilus sabuli Hezbri et al. 2015 is represented by BMG 8133, DSM 46844 and CECT 8820.
As in many other cases, here BMG 8133 is the original strain designation used in the laboratory or institution that conducted the taxon description and whose members (potentially in collaboration with other institutions) proposed the taxon name. DSM 46844 and CECT 8820 are deposits in culture collections, which are needed to validly publish the taxon name.
Version 1 is hierarchical, as DSM 46844 and CECT 8820 are treated as subordinate to BMG 8133. In version 1, BMG 8133 is a superordinate identifier that could be used in place of the subordinate identifiers DSM 46844 and CECT 8820; it would just be less specific.
In contrast, version 2 is flat. In version 2, all three identifiers have the same rank and are equally specific.
Which representation is preferable? There are a number of reasons to prefer version 2 over version 1 in a database such as LPSN:
  • Original strain designations distinct from identifiers in culture collections may be missing right away, particularly if the taxon name is proposed as the result of a re-evaluation of already established collection deposits.
  • Original strain designations may not be passed to the newer taxon name if a new combination is proposed, as only the deposits in culture collections are needed to validly publish a name.
  • The original strain designation can be regarded as an identifier for the strain within the institution that proposed the strain. There is no fundamental difference to identifiers used within culture collections. Accessibility may differ, of course, but accessibility may also differ between culture collections and within a culture collection over time.
  • Whereas the original strain designation can be regarded as an identifier for the strain within the original institution, version 1 would either lack such an identifier or use an identifier that is identical to the superordinate identifier. Both interpretations are disadvantageous.
  • The transfer between institutions does not generate a hierarchical relationship. If a copy is identical to the original, there is no reason to regard the copy as subordinate to the original. If otherwise, one would need to treat some collection identifiers as subordinate to another collection identifier if the former deposit was obtained from the latter deposit. Undoubtedly, strain histories have to be represented as ordered graphs. But the interpretation of such an ordered graph as a hierarchical relationship would generate problems of its own. Moreover, this alleged hierarchical relationship could in many cases not be expressed just by treating the original strain designation as superordinate identifier.
  • To express the equivalence relationship between distinct deposits of the same type strain, a superordinate name is not needed.
  • Version 2 more strongly encourages authors to use the most specific identifier available. This is of huge practical relevance, as allegedly equivalent deposits may later on turn out to be not equivalent.
The representation of type strains in LPSN thus uses version 2. Analogous arguments could be made for strains that are not type strains.