SUMMARY: The SeqCode removes the incentive to cultivate and deposit from prokaryotic nomenclature, reduces scientific replicability, undermines a scientific standard, and is fundamentally unfair, giving equal status to names based on the accessible organism itself and names based solely on experimental results. The ICSP should not accept the SeqCode but ratify a more suitable alternative, the "Best of Both Worlds".

In February 2020, many microbiologists urged the International Committee on Systematics of Prokaryotes (ICSP) not to adopt a proposed change to the International Code of Nomenclature of Prokaryotes (ICNP).

This change implied that a genome sequence (and potentially even a single gene sequence) could be accepted as the nomenclatural type of a species or subspecies with a validly published name. Previously, valid publication of a species or subspecies name under the ICNP required the deposition of a strain, the type strain, in two different culture collections in two different countries. This proposed shift from physical specimens - living organisms - to experimental data - genome sequences - as nomenclatural types would have fundamentally changed prokaryotic nomenclature. Several arguments were put forward against this change.

The ICSP rejected the proposal by a clear majority (17:6).

Unfortunately, this ICSP decision led to the publication of the "Code of Nomenclature of Prokaryotes Described from DNA Sequence Data" or "SeqCode" in 2022. This code not only contravenes the ICNP, but also suffers from essentially the same flaws as the proposal rejected by the ICSP in 2020.

We have serious concerns not only about the existence of two competing prokaryotic nomenclature codes, but also about the negative impact of the SeqCode on the incentive to cultivate and deposit, and the unfair idea of giving equal status to names based on the accessible organism itself and names based on experimental results (genome sequences), which should always be subject to correction and supplementation.

Almost all of the arguments made in 2020 apply equally to the SeqCode. Moreover, additional advances have been made in culturomics since 2020. Furthermore, "validly publishing" a name under the SeqCode because the type strain cannot be deposited under Rule 30 of the ICNP due to legal restrictions in the country of origin does not solve the underlying problem. Other researchers could still not replicate the study of the strain because it was not accessible. Only the adoption of more science-friendly laws in these countries would be a proper solution to the problem.

Arahal et al. proposed an approach called "Best of Both Worlds" in 2024. If adopted by the ICSP, this approach would not change the requirements for valid publication but would regulate Candidatus names in the same way as validly published names. Specifically, adoption of the "Best of Both Worlds" proposal by Arahal et al. (2024) would extend the ICNP to ensure that:

• It is formally regulated which Candidatus name applies in the case of synonyms.
• Homonyms between centrally registered Candidatus names and validly published names are avoided.
• Candidatus names are reused as soon as a name for the same taxon is proposed for valid publication.
• Authors of a Candidatus name continue to be recognized once a name for the same taxon is proposed for valid publication.

In this way, the "Best of Both Worlds" approach demonstrates that it is not necessary to lower the requirements for valid publication in order to comprehensively regulate the nomenclature of prokaryotes for which cultures are not yet available - or cannot be satisfactorily deposited. We appreciate this approach. In particular, we note that the "Best of Both Worlds" approach recognizes the work of those who formally propose Candidatus names as a result of metagenomic or other studies, as well as the work of those who later cultivate and deposit the same taxa.

This seems to be the fairest approach, meeting everyone's needs, recognizing everyone's contribution, and giving due consideration to the superiority of living cultures over sequences—even genome sequences—as nomenclatural types. In the "Best of Both Worlds," there would still be sufficient incentive to cultivate and deposit, which is urgently needed to ensure scientific replicability, the possibility to assess and augment sequence-derived results by phenotypic tests, and the availability of cultures for future generations.

The "Best of Both Worlds" is a much-needed compromise that has the potential to restore a unified code of nomenclature for prokaryotes. Such a compromise is preferable to the SeqCode, whose disadvantages—comprehensively listed by Arahal et al.—are largely the same as those of the proposal rejected by the ICSP in 2020, in addition to being in conflict with the ICNP.

We recommend that the ICSP adopt the "Best of Both Worlds" proposal.