ArticleNature biotechnology2020
A complete domain-to-species taxonomy for Bacteria and Archaea.
Article in Nature biotechnology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 815 papers.
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Who cites it
815 citing papers in PubMed.
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- Consistent diversity loss but divergent functional responses of freshwater biofilms to salinity and nutrient enrichment across climatic regions.Proceedings. Biological sciences · 2026Article
- Two D-loop resolution systems enable natural genetic transformation in bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Fast and accurate taxonomic domain assignment of short metagenomic reads using BBERT.Nucleic acids research · 2026Article
- Novel Antarctic chemolithotroph drives iron biomineralization.Microbiome · 2026Article
- Stability in flexibility: Shifting alliances stabilize the symbioses of marine animals over 150 million years.Science advances · 2026Article
- Comparing the Performance of Double-Stranded and Single-Stranded DNA Libraries for Ancient Oral Microbiome Reconstruction.Molecular ecology resources · 2026Article
- What is in the Dust? Species-Level Profiling Reveals Pathogenic and Protective Potential of Microbial Communities in Daycare and Home Environments.Environmental microbiology reports · 2026Article
- Functional-Taxonomic Scaling Resolves Conflicting Average Genome Size Estimates Across Environmental Gradients.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Species and strain sharing in the vaginal microbiome of mothers and their adult daughters.Cell reports · 2026Article
- Resilience of blue carbon microbiomes in response to ecological and anthropogenic filtering.Nature communications · 2026Article
- Longitudinal Stability of the Gut Microbiota in Relapsing-Remitting Multiple Sclerosis: A Prospective Observational Study.Microorganisms · 2026Article
- Novel Thermophilic Species ofLife (Basel, Switzerland) · 2026Article
- Antimicrobial Resistance and Associated Genetic Determinants ofAntibiotics (Basel, Switzerland) · 2026Article
- Ageing processes in the bonobo gut microbiome mirror human patterns.NPJ biofilms and microbiomes · 2026Article
- Age, strain, and gut section shape the microbiome of commercial laying hens.Poultry science · 2026Article
- Integrated multi-omics decipher the complex nodule microbiota and distinct Frankiaceae symbiotic traits in wild actinorhizal plants.The New phytologist · 2026Article
- Conformational diversity in poly-HAMP arrays and its implications for signal transduction.Protein science : a publication of the Protein Society · 2026Article
755 more citing papers are in PubMed but not listed here.
Corrections and comments
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- Erratum issued
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.