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 M. Chuvochina and D. Waite and Christian Rinke and Adam Skarshewski and Pierre-Alain Chaumeil and P. 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…Expand

Paper Mentions

Interventional Clinical Trial
Nitrate is a controversial component of vegetables, meat, and drinking water. The now well-established benefits of nitrate, through the enterosalivary nitrate-nitrite-nitric oxide… Expand
ConditionsHealth Risk Behaviors
InterventionDietary Supplement
A standardized archaeal taxonomy for the Genome Taxonomy Database.
TLDR
A standardized archaeal taxonomy is proposed that is derived from a 122-concatenated-protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence and is shown to robustly correct for substitution rates varying up to 30-fold using simulated datasets. Expand
A rank-normalized archaeal taxonomy based on genome phylogeny resolves widespread incomplete and uneven classifications
TLDR
A standardized archaeal taxonomy is proposed, as part of the Genome Taxonomy Database (GTDB), derived from a 122 concatenated protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence. Expand
A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny
TLDR
By examining the relative evolutionary divergence of taxonomic groups of equivalent rank, it is found that fungal taxonomy is broadly aligned with genome sequence divergence, but also identified lineages, such as the subphylum Saccharomycotina, where current taxonomic circumscription does not fully account for their high levels of evolutionary divergence. Expand
Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy
TLDR
A standardized archaeal taxonomy is proposed, as part of the Genome Taxonomy Database (GTDB), derived from a 122 concatenated protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence (RED). Expand
Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas
TLDR
This work presents as a model the currently accepted taxonomy of the genus Pseudomonas and how it can be modified when new taxonomic methodologies are applied, and the boundaries of the species in the genus are discussed based on phylogenomic analyses in relation to other genera in the family pseudomonadaceae. Expand
A complete domain-to-species taxonomy for Bacteria and Archaea
TLDR
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. Expand
A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy
TLDR
It is determined that the analysis of the Genome Taxonomy Database still results in classification boundary blur between some genera and that the marker gene-based approach has limitations, and methods based on genomic alignment should be considered for use for species classification. Expand
Quantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of Life
TLDR
This work quantified the relative abundances of clusters of orthologous group functional categories (COG-FCs) as a proxy for traits within the lineages of 13,735 cultured and uncultured microbial lineages from a custom-curated genome database, the first work to quantify the variance in metabolic potential contributed by individual taxonomic ranks. Expand
A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index
TLDR
Genetic coherence is an emergent property of genera in Bacteria and Archaea that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species in this study. Expand
Quantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of Life
TLDR
Cluster of orthologous group functional categories is adopted as a scheme to describe the genomic contents of microbes, which can be applied to any microbial lineage for which genomes are available and demonstrates statistically significant patterns in cluster of Orthologous Group functional categories at the taxonomic levels spanning from domain to genus. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 94 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. Expand
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. Expand
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. Expand
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. Expand
Insights into the phylogeny and coding potential of microbial dark matter
TLDR
This study applies single-cell genomics to target and sequence 201 archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life and provides a systematic step towards a better understanding of biological evolution on the authors' planet. Expand
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). Expand
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. Expand
Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups
TLDR
An automated protocol for identifying potential PhyEco markers from a set of complete genome sequences is described, which combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. Expand
The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains.
TLDR
The signing authors together with the journal Systematic and Applied Microbiology (SAM) have started an ambitious project to reconstruct a single 16S rRNA tree harboring all sequenced type strains of the hitherto classified species of Archaea and Bacteria. Expand
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. Expand
...
1
2
3
4
5
...