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

Nature Biotechnology volume 38, pages 1079–1086 (2020)Cite this article

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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.

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Fig. 1: Overview of workflow for organizing genome assemblies into species clusters.
Fig. 2: Properties of genomes selected as species representatives.
Fig. 3: Illustrative examples of circumscribing species for varying ANI values between species representatives.
Fig. 4: Key properties of GTDB species clusters circumscribed by ANI to a representative genome.
Fig. 5: Comparison of proposed species assignments with the NCBI taxonomy.

Data availability

Genome metadata used to establish the proposed species clusters are available on the GTDB website in the files ar122_metadata.tsv and bac120_metadata.tsv. Metadata for the 24,706 GTDB species representatives are in the file sp_clusters.tsv. Genomes in the GTDB satisfying the high-quality MIMAG criteria47 are indicated in the file hq_mimag_genomes.tsv. Genome sequences are available from the NCBI Assembly database, including the 153 archaeal MAGs in BioProject PRJNA593905.

Code availability

The methodology used to establish the GTDB species clusters is implemented in version GTDB-R89 of the GTDB Species Cluster Toolkit (https://github.com/Ecogenomics/gtdb-species-clusters), a Python program available under the GNU General Public License v.3.0.

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Acknowledgements

We thank the members of an NSF-sponsored Microbial Taxonomy Workshop (NSF no. 1841658) for helpful discussions relating to establishing species clusters. This project was supported by an Australian Research Council Laureate Fellowship (grant no. FL150100038) awarded to P.H. and an Australian Research Council Future Fellowship (grant no. FT170100213) awarded to C.R.

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Authors and Affiliations

  1. Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia

    Donovan H. Parks, Maria Chuvochina, Pierre-Alain Chaumeil, Christian Rinke, Aaron J. Mussig & Philip Hugenholtz

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  1. Donovan H. Parks
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Contributions

D.H.P. and P.H. wrote the paper with constructive suggestions from all other authors. D.H.P. designed the initial study. M.C., C.R. and P.H. provided nomenclatural advice and manual curation of species representatives where necessary. D.H.P., P.-A.C. and A.J.M. performed the bioinformatic analyses.

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Correspondence to Donovan H. Parks.

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Supplementary information

Supplementary Information

Supplementary Fig. 1 and Tables 1–3, 5, 7, 8, 11, 14, 15, 17 and 19.

Reporting Summary

Supplementary Table 4

Genomes satisfying the assignment criteria of multiple species with validly or effectively published names

Supplementary Table 6

Species reclassified as synonyms because they have an ANI > 97% to a species with naming priority

Supplementary Table 9

Species where the difference in the mean ANI from the medoid and mean ANI from the GTDB-selected representative is >2

Supplementary Table 10

Genomes satisfying the assignment criteria for multiple GTDB species clusters

Supplementary Table 12

Species clusters that were incongruent with the proposed species clusters across all five trials evaluating the impact of forming species clusters from randomly selected representative genomes

Supplementary Table 13

Evaluation of the monophyly of the proposed species clusters

Supplementary Table 16

GTDB and NCBI species assignments for the 24,080 proposed representative genomes with a species classification in the NCBI taxonomy

Supplementary Table 18

List of 87 genomes retained in the genome dataset despite failing the QC criteria as they represent genomes of high nomenclatural or taxonomic importance

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Parks, D.H., Chuvochina, M., Chaumeil, PA. et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol 38, 1079–1086 (2020). https://doi.org/10.1038/s41587-020-0501-8

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