Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

Whitman, William B.; Chuvochina, Maria; Hedlund, Brian P.; Hugenholtz, Philip; Konstantinidis, Konstantinos T.; Murray, Alison E.; Palmer, Marike; Parks, Donovan H.; Probst, Alexander J.; Reysenbach, Anna‐Louise; Rodriguez‐R, Luis M.; Rosselló‐Móra, Ramon; Sutcliffe, Iain C.; Venter, Stephanus

doi:10.1016/j.syapm.2022.126305

Cited by 34 publications

(20 citation statements)

References 68 publications

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“…The SeqCode uses genome sequence data as common currency for typification of both cultivated and uncultivated microorganisms and follows rules similar to those of the ICNP for priority 9 . In essence, the rules of both codes state that the earliest validly published name for a taxon in a particular position is the correct name (has priority), observing historical precedent and stabilizing nomenclature.…”

Section: Resultsmentioning

confidence: 99%

SeqCode: a nomenclatural code for prokaryotes described from sequence data

et al. 2022

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Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.

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Section: Resultsmentioning

confidence: 99%

SeqCode: a nomenclatural code for prokaryotes described from sequence data

et al. 2022

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“…The GTDB's exclusion of subspecies could potentially have far-reaching significance because its classification system is utilized as the taxonomic framework for the current edition of Bergey's Manual of Systematics of Archaea and Bacteria [ 62 ]. Our approach of distinguishing between core and accessory genomes when demarcating taxa and varieties also resonates with the newly proposed SeqCode [ 63 , 64 ] where high quality metagenome assembled genomes (MAGs) will be acknowledged as suitable permanent types for the description of prokaryotic species. However, to ensure consistency with the ICNP and to accommodate community feedback during the SeqCode's development, this new taxonomic initiative also allows for the description of subspecies.…”

Section: What Are the Implications Of Abandoning Subspecies As Taxono...mentioning

confidence: 55%

Relevance of prokaryotic subspecies in the age of genomics

Venter

Palmer²,

Steenkamp³

2022

New Microbes and New Infections

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“…New bacterial descriptions are also constrained by journal capabilities (Tamames and Rosselló-Móra, 2012). In order to give an identity to the mass of uncultured microorganisms, the availability of a pure culture is maybe not Whitman et al, 2022). The requirements of a pure axenic culture of the ICNP as the only type material possible for naming new microbial species has been criticized as self-limiting, hindering microbiological research and raising the costs associated with naming new taxa (Palmer et al, 2022).…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

2023

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In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial “dark matter” hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.

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Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

Cited by 34 publications

References 68 publications

SeqCode: a nomenclatural code for prokaryotes described from sequence data

SeqCode: a nomenclatural code for prokaryotes described from sequence data

Relevance of prokaryotic subspecies in the age of genomics

Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

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