Type strains

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

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 name 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:

  • Version 2 is the one used by the ICNP, which states: "In the case of species and subspecies, the type strain [...] should be designated by the author’s strain number as well as the accession number under which it is held by at least one culture collection from which cultures of the strain are available" [Appendix 7 (5)]. That is, "the author’s strain number" (e.g., BMG 8133) designates the strain and "the accession number under which it is held by at least one culture collection" (e.g., DSM 46844) designates the strain; there is no principal difference. See also Rule 18c Note 1: "The term ‘strain’ refers to the culture or subcultures of it, described in the original description." Note the plural. Analogous information is given in appendix 10A (3) of the ICNP.
  • Referring to the example given above, the phrasing as used in most taxon descriptions would be "The type strain is BMG 8133 (= DSM 46844 = CECT 8820)." Here the parentheses could be misunderstood as indicating the superordinate position of BMG 8133. However, the equals signs indicate equivalence, and the parentheses are often missing in the literature. They are also missing in several examples given in the ICNP.
  • Original strain names 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 names 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 name 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 name 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 name 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.

Databases also differ regarding the usage of the term "proposed type strain" for type strains of names of species or subspecies that are not validly published.

The ICNP does neither use nor define the term "proposed type strain". It is actually in conflict with the ICNP to assume that a "proposed type strain" becomes a "type strain" once the name for which this strain serves as the nomenclatural type becomes validly published. Since having a type strain (as opposed to having a "proposed type strain") is a prerequisite for names of species and names of subspecies to become validly published [Rule 27(3); Rule 16; Rule 15], the valid publication of a name cannot in turn be a prerequisite for a "proposed type strain" to become a type strain.

Moreover, Rule 18b states: "If the author in the effective publication of the name of a species or subspecies definitely designated a type strain, then this strain shall be accepted as the type strain and may be referred to as the holotype." The rule does not refer to the effective publication having designated a "proposed type strain"; the rule says "type strain". In fact, if the type strain designated in the effective publication was just a "proposed type strain", it would have preliminary status and thus there would not be any need to accept it, contrary to the Rule. It is obvious from Rule 18c that the INCP uses the term "proposed" to indicate the preliminary status of an entity, as a "proposed neotype" can be appealed against. Contrast this with Rule 18b, which determines that a designated type strain has to be accepted and thus cannot be appealed against. Since the effective publication of a name may precede the valid publication of a name [Rule 27 (2)] it is not in accordance with the ICNP to assume that the valid publication of a name changes a "proposed type strain" to a type strain.

The idea that a "proposed type strain" becomes a type strain via the valid publication of the name of the species or subspecies for which it serves as the nomenclatural type may originate from a misinterpretation of the status of not being validly published. In the ICNP valid publication solely refers to names of taxa but not to names or numbers of strains. If the type strain designated by the authors of the effective publication does not fulfill the conditions specified by the ICNP, then the name of the species or subspecies for which it serves as the nomenclatural type simply does not become validly published.

LPSN thus does not use the term "proposed type strain" because it is misleading.

This LPSN page was printed on 2024-02-21 07:19:32