A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

By Donovan H. Parks, Maria Chuvochina, D. Waite, Christian Rinke, Adam Skarshewski, Pierre-Alain Chaumeil, Philip Hugenholtz. Nature Biotechnology, 2018

2,997 citations recorded by the source corpus.

Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5b0403e1f4b997e411bac2fb930842fae71a785a

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Citations in the corpus

The Gut Microbiota and Inflammation: An Overview (2020, background): “Organisms that are within the same lower taxonomic rank groups have greater genetic sequence similarities, indicative of more recent evolutionary divergence [7].”
RESCRIPt: Reproducible sequence taxonomy reference database management (2020, methodology): “The GTDB extracts and curates data from both NCBI-RefSeq and NCBI-GenBank to generate a phylogeny of Archaea and Bacteria from roughly 120 ubiquitous single-copy proteins [24,93].”
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT (2019, positive): “Even though the true distance between taxonomic ranks may vary [39], calculating mean taxonomic rank in this fashion does serve as a proxy to show that classifications are called at higher taxonomic ranks “on average” under certain parameter conditions or, e.”
Linking metagenomics to aquatic microbial ecology and biogeochemical cycles (2019, background): “…bacterial MAG reconstructions from deep aquifers and other environments has dramatically increased known phylum level diversity by discovery of the Candidate Phylum Radiation within the bacterial domain (Brown et al. 2015; Hug et al. 2016), and a revised phylogeny of bacteria (Parks et al. 2018).”
AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential (2019, background): “fr (27) and GTDB (28), autoMLST automates all steps in the process including organism and gene selection, offers de novo construction of maximum-likelihood trees, and includes useful features such as model finding and tree annotations.”
IQ-TREE 3: phylogenomic inference software using complex evolutionary models (2026, neutral): “These studies range from inferring ancient relationships within Bacteria (Parks et al. 2018; Wehbi et al. 2024), Archaea (Alves et al. 2018; Dombrowski et al. 2020), and eukaryotes (Burki et al. 2016; Williamson et al. 2025); to more recent divergences among plants (Puttick et al. 2018), animals…”