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. 2022 Jun 1:47:100991.
doi: 10.1016/j.nmni.2022.100991. eCollection 2022 Apr-May.

It is time for a new type of type to facilitate naming the microbial world

Affiliations

It is time for a new type of type to facilitate naming the microbial world

M Palmer et al. New Microbes New Infect. .

Abstract

Since January 1, 2001, the only acceptable nomenclatural type for species under the International Code of Nomenclature of Prokaryotes (ICNP) has been pure cultures. Here, we argue that this requirement is discordant with the more inclusive nature of nomenclatural types accepted under other codes of nomenclature and posit that the unique rigidity of the ICNP has failed to serve the broad research community and has stifled progress. This case is based on the axiom that many archaea and bacteria are interdependent in nature and therefore difficult, if not impossible, to grow, preserve, and distribute as pure cultures. As such, a large proportion of Earth's biodiversity cannot be named under the current system, which limits our ability to communicate about microbial diversity within and beyond the microbiology research community. Genome sequence data are now encouraged for valid publication of new taxa in microbial systematics journals, and metagenome-assembled genomes and single cell-amplified genomes are being generated rapidly from every biome on Earth. Thus, genome sequences are available for both cultivated and uncultivated microorganisms and can readily serve as a new category of nomenclatural type, allowing for a unified nomenclature for all archaea and bacteria, whether or not they are available as pure cultures. Ideally this would be under a single code of nomenclature but, as we review here, the newly established SeqCode will operate in parallel with the ICNP as a first step toward this goal.

Keywords: ICNP; SeqCode; Systematics; genomics; metagenomics; nomenclatural type; single-cell genomics; taxonomy; type.

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Figures

Fig. 1
Fig. 1
Different types of types. Examples of categories of types acceptable under different codes of nomenclature. (A) Tyrannosaurus rex holotype specimen CM 9380/AMNH 973 at the Carnegie Museum of Natural History, originally collected from the Hell Creek Formation, Montana, USA. Although the skeleton was <25% complete, it is sufficient to identify the species. (Photo: Wikimedia Commons.) (B) Finch types collected in the Galapagos Islands by Darwin during the second voyage of the HMS Beagle in the 1830s, used with permission from the Natural History Museum in London. (C) Paratype slide of the ciliate Euplotes rariseta, compliments of Emma Sherlock of the Natural History Museum in London. (D) Herbarium type sheet for Acer saccharum, commonly known as sugar maple. Photo: Wikimedia Commons. (E) Lyophilized culture of Kallotenue papyrolyticumDSM 26889T [48] from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ). Currently, viable axenic cultures are the only category of nomenclatural type acceptable under the ICNP. (F) Representation of the whole genome of Thermus oshimai JL-2 in comparison with two other T. oshimai genomes; high-quality genome sequence data would be eligible under the SeqCode, which is under development. (Image reproduced from [49]).
Fig. 2
Fig. 2
Validly published species names. Names per “kingdom” according to the Catalogue of Life 2019 Annual Checklist. Data for Archaea + Bacteria and viruses were updated per the LPSN count of validly published species names without synonyms plus 2020 cyanobacterial species names listed in the Botanical Code section, which will be validated under the ICNP (updated 4/6/2022) and per the ICTV Master Species Lists 2020. v1 (9110).

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