A complete domain-to-species taxonomy for Bacteria and Archaea - PubMed (original) (raw)

. 2020 Sep;38(9):1079-1086.

doi: 10.1038/s41587-020-0501-8. Epub 2020 Apr 27.

Affiliations

• PMID: 32341564
• DOI: 10.1038/s41587-020-0501-8

A complete domain-to-species taxonomy for Bacteria and Archaea

Donovan H Parks et al. Nat Biotechnol. 2020 Sep.

Erratum in

• Author Correction: A complete domain-to-species taxonomy for Bacteria and Archaea.
  Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P. Parks DH, et al. Nat Biotechnol. 2020 Sep;38(9):1098. doi: 10.1038/s41587-020-0539-7. Nat Biotechnol. 2020. PMID: 32887961

Abstract

The Genome Taxonomy Database is a phylogenetically consistent, genome-based taxonomy that provides rank-normalized classifications for ~150,000 bacterial and archaeal genomes from domain to genus. However, almost 40% of the genomes in the Genome Taxonomy Database lack a species name. We address this limitation by using commonly accepted average nucleotide identity criteria to set bounds on species and propose species clusters that encompass all publicly available bacterial and archaeal genomes. Unlike previous average nucleotide identity studies, we chose a single representative genome to serve as the effective nomenclatural 'type' defining each species. Of the 24,706 proposed species clusters, 8,792 are based on published names. We assigned placeholder names to the remaining 15,914 species clusters to provide names to the growing number of genomes from uncultivated species. This resource provides a complete domain-to-species taxonomic framework for bacterial and archaeal genomes, which will facilitate research on uncultivated species and improve communication of scientific results.

PubMed Disclaimer

Comment in

• Taxonomy of Bacteria and Archaea.
  Tang L. Tang L. Nat Methods. 2020 Jun;17(6):562. doi: 10.1038/s41592-020-0863-3. Nat Methods. 2020. PMID: 32499624 No abstract available.
• Genome-based Taxonomy for Bacteria: A Recent Advance.
  Zong Z. Zong Z. Trends Microbiol. 2020 Nov;28(11):871-874. doi: 10.1016/j.tim.2020.09.007. Epub 2020 Sep 24. Trends Microbiol. 2020. PMID: 32980201

References

1. 1. Kyrpides, N. C. et al. Genomic Encyclopedia of Bacteria and Archaea: sequencing a myriad of type strains. PLoS Biol. 12, e1001920 (2014). - PubMed - PMC - DOI
2. 1. Mukherjee, S. et al. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nat. Biotechnol. 35, 676–683 (2017). - PubMed - DOI
3. 1. Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2, 1533–1542 (2017). - PubMed - DOI
4. 1. Chen, I. A. et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 47, D666–D677 (2019). - PubMed - DOI
5. 1. Pasolli, E. et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell 176, 649–662 (2019). - PubMed - PMC - DOI

Publication types

MeSH terms

LinkOut - more resources

• Full Text Sources

  • Nature Publishing Group

• Other Literature Sources

  • H1 Connect