SeqCode Publications

Brian P. Hedlund, Maria Chuvochina, Philip Hugenholtz, Konstantinos T. Konstantinidis, Alison E. Murray, Marike Palmer, Donovan H. Parks, Alexander J. Probst, Anna-Louise Reysenbach, Luis M. Rodriguez-R, Ramon Rossello-Mora, Iain C. Sutcliffe, Stephanus N. Venter, and William B. Whitman. Nature Microbiology (2022). https://doi.org/10.1038/s41564-022-01214-9

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.

William B Whitman, Maria Chuvochina, Brian P Hedlund, Philip Hugenholtz, Kostas T Konstantinidis, Alison Murray, Marike Palmer, Donovan H Parks, Alexander J Probst, Anna-Louise Reysenbach, Luis M Rodriguez-R, Ramon Rossello-Mora, Iain Sutcliffe, and Stephanus N Venter. Systematic and Applied Microbiology (2022). https://doi.org/10.1016/j.syapm.2022.126305

Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.

William B. Whitman, Brian P. Hedlund, Marike Palmer, Iain Sutcliffe, and Maria Chuvochina. ISME Communications (2023). https://doi.org/10.1038/s43705-023-00303-y

Edited by William B Whitman, Maria Chuvochina, Brian P Hedlund, Philip Hugenholtz, Kostas T Konstantinidis, Alison Murray, Marike Palmer, Donovan H Parks, Alexander J Probst, Anna-Louise Reysenbach, Luis M Rodriguez-R, Ramon Rossello-Mora, Iain Sutcliffe, and Stephanus N Venter.