The DOI matches its Crossref record; 61 of the 61 references it cites were found in a registry or an index.
A complete domain-to-species taxonomy for Bacteria and Archaea
Open accessAbstract
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. A full species classification is built for all publicly available bacterial and archaeal genomes.
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Cites
Prodigal: prokaryotic gene recognition and translation initiation site identification
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Self-citationAccelerated Profile HMM Searches
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Self-citationDNA–DNA hybridization values and their relationship to whole-genome sequence similarities
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Cited by
Parks, D. H., Chuvochina, M., Rinke, C., Mussig, A. J., Chaumeil, P.-A., & Hugenholtz, P. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab776 · Cited by 2,402
Self-citationBlanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., Manghi, P., Dubois, L., Huang, K. D., Thomas, A. M., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01688-w · Cited by 1,442
RESCRIPt: Reproducible sequence taxonomy reference database management
(2021) · doi:10.1371/journal.pcbi.1009581 · Cited by 983
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut
Gregory, A. C., Zablocki, O., Zayed, A. A., Howell, A., Bolduc, B., & Sullivan, M. B. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.08.003 · Cited by 658
Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project
Lopera-Maya, E. A., Kurilshikov, A., van der Graaf, A., Hu, S., Andreu-Sánchez, S., Chen, L., Vila, A. V., Gacesa, R., Sinha, T., Collij, V., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-00992-y · Cited by 553
Metadata
- Authors
- Parks, D. H., Chuvochina, M., Chaumeil, P.-A., Rinke, C., Mussig, A. J., & Hugenholtz, P.
- Venue
- Nature Biotechnology
- Published
- 2020-04-27
- Volume
- 38
- Issue
- 9
- Pages
- 1079-1086
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W3019706413
- Cited by
- 1,530
- References
- 61
- FWCI
- 62.86
- Type
- journal article
- Language
- en
- Open access
- green
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