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

@article{Parks2018ASB,
  title={A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life},
  author={Donovan H. Parks and Maria Chuvochina and David W. Waite and Christian Rinke and Adam Skarshewski and Pierre-Alain Chaumeil and P. Bernt Hugenholtz},
  journal={Nature Biotechnology},
  year={2018},
  volume={36},
  pages={996-1004}
}
Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. [] Key Method 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…
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References

SHOWING 1-10 OF 100 REFERENCES
Genome-Based Taxonomic Classification of Bacteroidetes
TLDR
A large collection of type-strain genomes from Bacteroidetes and closely related phyla are assessed based on the principles of phylogenetic classification and trees inferred from genome-scale data and corrected G+C content values have a significantly better fit to the phylogeny.
Towards a Genome-Based Taxonomy for Prokaryotes
TLDR
The AAI-based approach provides a means to evaluate the robustness of alternative genetic markers for phylogenetic purposes, and could contribute significantly to a genome-based taxonomy for all microbial organisms.
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
TLDR
A ‘taxonomy to tree’ approach for transferring group names from an existing taxonomy to a tree topology is developed and used to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences.
Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices
TLDR
It is concluded that the current best approach for generating a single phylogenetic tree, suitable for use as a reference phylogeny for comparative analyses, is to perform a maximum likelihood analysis of a concatenated alignment of conserved, single-copy genes.
Unusual biology across a group comprising more than 15% of domain Bacteria
TLDR
This work reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria, infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR).
Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies
TLDR
An integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences, with accompanying bioinformatics tools.
Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria
TLDR
By modeling the expansion of pan-genomes and analyzing core and flexible genes, this study provides snapshots on how the complex processes of gene acquisition, conservation, and removal affect the evolution of different species, and contribute to the metabolic diversity and versatility of Epsilonproteobacteria.
TreeOTU: Operational Taxonomic Unit Classification Based on Phylogenetic Trees
TLDR
The development of TreeOTU, a phylogenetic tree structure based OTU classification method that takes into account differences in rates of evolution between taxa and between genes is reported here.
Genome-Based Microbial Taxonomy Coming of Age.
TLDR
Concerted efforts are now needed to synthesize and integrate the burgeoning genomic data resources into a coherent universal tree of life and genome-based taxonomy, akin to the completion of the periodic table.
...
...