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SeqCode: a nomenclatural code for prokaryotes described from sequence data.

Brian P Hedlund1, Maria Chuvochina2, Philip Hugenholtz2

  • 1School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA.

Nature Microbiology
|September 19, 2022
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Summary
This summary is machine-generated.

The new SeqCode allows naming prokaryotes using genome sequences when pure cultures are unavailable, addressing a major limitation in microbial nomenclature. This system ensures reproducible naming for all prokaryotes, cultivable or not.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Taxonomy

Background:

  • Most prokaryotes cannot be pure cultured, preventing their formal naming under current rules.
  • The International Code of Nomenclature of Prokaryotes (ICNP) relies on cultivable organisms, excluding a vast majority of microbes.
  • A need exists for a standardized nomenclature system applicable to unculturable prokaryotes.

Purpose of the Study:

  • To introduce and describe the SeqCode, a novel system for prokaryotic nomenclature.
  • To enable the valid publication of prokaryotic names using genome sequences as types.
  • To establish a framework for naming both isolated and uncultured prokaryotes.

Main Methods:

  • Development of the SeqCode, a set of rules for prokaryotic nomenclature based on genome sequences.
  • Utilization of the SeqCode Registry for registration, validation, and metadata linking of names and types.
  • Description of two registration pathways for names, including Candidatus names.

Main Results:

  • The SeqCode allows valid naming of prokaryotes using isolate genomes, metagenome-assembled genomes, and single-amplified genomes.
  • The SeqCode Registry serves as a central portal for managing prokaryotic names and their associated sequence data.
  • Recommendations for minimal DNA sequence standards for nomenclature are provided.

Conclusions:

  • The SeqCode offers a reproducible and objective method for prokaryotic nomenclature, irrespective of cultivability.
  • This system expands the scope of formal prokaryotic naming to include previously unnameable organisms.
  • The SeqCode facilitates standardized communication and data sharing across microbiological disciplines.