Content | |
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Description | Proposed prokaryotic nomenclature |
Contact | |
Research center | Australian Centre for Ecogenomics, University of Queensland |
Authors | Phil Hugenholtz, Maria Chuvochina, Christian Rinke |
Primary citation | PMID 30148503 |
Release date | 2018 |
Access | |
Website | https://gtdb.ecogenomic.org/ |
Miscellaneous | |
License | CC BY-SA 4.0 |
Version | R07/RS207 (8 April 2022) |
Curation policy | mixed |
The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed nomenclature of prokaryotes, following a phylogenomic approach based on a set of conserved single-copy proteins. In addition to resolving paraphyletic groups, this method also reassigns taxonomic ranks algorithmically, updating names in both cases. [1] Information for archaea was added in 2020, [2] along with a species classification based on average nucleotide identity. [3] Each update incorporates new genomes as well as automated and manual curation of the taxonomy. [4]
An open-source tool called GTDB-Tk is available to classify draft genomes into the GTDB hierarchy. [5] The GTDB system, via GTDB-Tk, has been used to catalogue not-yet-named bacteria in the human gut microbiome and other metagenomic sources. [6] [7]
The GTDB is incorporated into the Bergey's Manual of Systematics of Archaea and Bacteria in 2019 as its phylogenomic resource. [8]
Nanoarchaeota is a proposed phylum in the domain Archaea that currently has only one representative, Nanoarchaeum equitans, which was discovered in a submarine hydrothermal vent and first described in 2002.
The Geobacteraceae are a family within the Thermodesulfobacteriota.
Desulfovibrionaceae is a family of bacteria belonging to the phylum Thermodesulfobacteriota.
Desulfohalobiaceae is a family of bacteria belonging to the phylum Thermodesulfobacteriota.
The Thermodesulfobacteriota are a phylum of thermophilic sulfate-reducing bacteria.
The Myxococcota are a phylum of bacteria known as the fruiting gliding bacteria. All species of this group are Gram-negative. They are predominantly aerobic genera that release myxospores in unfavorable environments.
Nanohaloarchaea is a clade of diminutive archaea with small genomes and limited metabolic capabilities, belonging to the DPANN archaea. They are ubiquitous in hypersaline habitats, which they share with the extremely halophilic haloarchaea.
In metagenomics, binning is the process of grouping reads or contigs and assigning them to individual genome. Binning methods can be based on either compositional features or alignment (similarity), or both.
The "Aigarchaeota" are a proposed archaeal phylum of which the main representative is Caldiarchaeum subterraneum. It is not yet clear if this represents a new phylum or a Nitrososphaerota order, since the genome of Caldiarchaeum subterraneum encodes several Nitrososphaerota-like features. The name "Aigarchaeota" comes from the Greek αυγή, avgí, meaning "dawn" or "aurora", for the intermediate features of hyperthermophilic and mesophilic life during the evolution of its lineage.
Parvarchaeota is a phylum of archaea belonging to the DPANN archaea. They have been discovered in acid mine drainage waters and later in marine sediments. The cells of these organisms are extremely small consistent with small genomes. Metagenomic techniques allow obtaining genomic sequences from non-cultured organisms, which were applied to determine this phylum.
Hadesarchaea, formerly called the South-African Gold Mine Miscellaneous Euryarchaeal Group, are a class of thermophile microorganisms that have been found in deep mines, hot springs, marine sediments, and other subterranean environments.
Syntrophus is a Gram negative bacterial genus from the family of Syntrophaceae.
DPANN is a superphylum of Archaea first proposed in 2013. Many members show novel signs of horizontal gene transfer from other domains of life. They are known as nanoarchaea or ultra-small archaea due to their smaller size (nanometric) compared to other archaea.
The candidate phyla radiation is a large evolutionary radiation of bacterial lineages whose members are mostly uncultivated and only known from metagenomics and single cell sequencing. They have been described as nanobacteria or ultra-small bacteria due to their reduced size (nanometric) compared to other bacteria.
NC10 is a bacterial phylum with candidate status, meaning its members remain uncultured to date. The difficulty in producing lab cultures may be linked to low growth rates and other limiting growth factors.
There are several models of the branching order of bacterial phyla, one of these is the Genome Taxonomy Database (GTDB).
Bdellovibrionota is a phylum of bacteria.