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

William B Whitman¹, Maria Chuvochina², Brian P Hedlund³

¹Department of Microbiology, University of Georgia, Athens, GA, USA.

Systematic and Applied Microbiology

|September 1, 2022

Summary

A new prokaryotic nomenclature code, SeqCode, enables naming organisms using DNA sequences, simplifying classification for both cultured and uncultured bacteria and archaea.

Area of Science:

Microbiology
Genomics
Bioinformatics

Background:

Genomics is now integral to prokaryotic systematics, with widespread use of genome sequencing for species delineation and phylogenomics for higher taxa classification.
Environmental genomics has uncovered extensive microbial diversity, including many uncultivated prokaryotes.
Current nomenclature systems face challenges in accommodating this genomic data and uncultured diversity.

Purpose of the Study:

To introduce the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), a novel framework for prokaryotic nomenclature.
To enable the naming of Archaea and Bacteria using DNA sequences as nomenclatural types.
To simplify prokaryotic nomenclature, making it more accessible and applicable to both cultured and uncultured taxa.

Main Methods:

Development of the SeqCode over two years, involving simplifications compared to the International Code of Nomenclature of Prokaryotes (ICNP).
Incorporation of DNA sequences as nomenclatural types, allowing naming based on genomic data.
Provisions for naming cultured organisms, including fastidious prokaryotes unsuitable for culture collections.

Main Results:

The SeqCode provides a mechanism for naming prokaryotes based on sequence data, addressing the limitations of traditional methods.
It facilitates the inclusion of uncultured taxa within formal nomenclature.
The code introduces simplifications to enhance accessibility and ease of application in prokaryotic systematics.

Conclusions:

The SeqCode offers a unified approach to prokaryotic classification, integrating genomic information and encompassing both cultured and uncultured organisms.
This new code is expected to facilitate the naming of taxa across diverse biomes and encourage the study of uncultivated prokaryotes.
SeqCode promotes interdisciplinary collaboration, advancing the comprehensive description of prokaryotic life.

Keywords:

Candidatus Metagenome Nomenclatural code Nomenclatural type SeqCode

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