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Related Concept Videos

Genomic DNA in Prokaryotes00:46

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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
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Options and considerations for validation of prokaryotic names under the SeqCode.

Stephanus N Venter1, Luis M Rodriguez-R2, Maria Chuvochina3

  • 1Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.

Systematic and Applied Microbiology
|September 21, 2024
PubMed
Summary

Formal naming of uncultured bacteria and archaea is crucial for understanding prokaryotic diversity and evolution. The new SeqCode offers a pathway to validate names for these microbes, moving beyond provisional identifiers.

Keywords:
CandidatusGenome Taxonomy DatabaseICNPNomenclatureNovel speciesSeqCode

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Area of Science:

  • Microbiology
  • Taxonomy
  • Bioinformatics

Background:

  • Stable taxon names are vital for cataloging prokaryotic diversity and facilitating scientific communication.
  • Current nomenclature, under the International Code of Nomenclature of Prokaryotes (ICNP), has successfully named only a fraction of estimated prokaryotic species, primarily those that are culturable.
  • The majority of prokaryotic species remain uncultured, hindering their formal classification and study.

Purpose of the Study:

  • To present options and considerations for validating names of uncultured prokaryotic taxa.
  • To introduce the recently established Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode) as a solution.
  • To encourage community engagement for the formal naming of the uncultured majority.

Main Methods:

  • Review of current prokaryotic nomenclature practices.
  • Exploration of the framework provided by the SeqCode.
  • Discussion of community engagement strategies for taxonomic specialists.

Main Results:

  • The ICNP has limitations in addressing the vast number of uncultured prokaryotes.
  • The SeqCode provides a mechanism for the formal validation of names based on sequence data.
  • Community involvement is identified as critical for the successful implementation of SeqCode.

Conclusions:

  • The SeqCode represents a significant advancement in prokaryotic taxonomy, enabling the formal naming of previously unclassifiable taxa.
  • Formalizing names for uncultured prokaryotes will enhance our understanding of microbial diversity and evolution.
  • Active participation from the scientific community is essential for the widespread adoption and success of SeqCode.