|
Branching Order Of Bacterial Phyla (Genome Taxonomy Database, 2018)
There are several models of the branching order of bacterial phyla, one of these is the Genome Taxonomy Database (GTDB). The GTDB is an initiative to establish a standardised microbial taxonomy based on genome phylogeny, primarily funded by an Australian Research Council Laureate Fellowship. The genomes used to construct the phylogeny are obtained from RefSeq and Genbank, and GTDB releases are indexed to RefSeq releases, starting with release 76. Importantly and increasingly, this dataset includes draft genomes of uncultured microorganisms obtained from metagenomes and single cells, ensuring improved genomic representation of the microbial world. All genomes are independently quality controlled using CheckM before inclusion in GTDB. The GTDB taxonomy is based on genome trees inferred with FastTree from an aligned concatenated set of 120 single copy marker proteins for Bacteria, and with IQ-TREE from a concatenated set of 53 (since RS207; 122 before) marker proteins for Archaea. Add ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genome Taxonomy Database
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 breaking up paraphyletic groups, this method also reassigns taxonomic ranks algorithmically, creating new names in both cases. Information for archaea was added in 2020, along with a species classification based on average nucleotide identity. Each update incorporates new genomes as well as human adjustments to the taxonomy. An open-source tool called GTDB-Tk is available to classify draft genomes into the GTDB hierarchy. The GTDB system, via GTDB-Tk, has been used to catalogue not-yet-named bacteria in the human gut microbiome and other metagenomic sources. The GTDB is incorporated into the ''Bergey's Manual of Systematics of Archaea and Bacteria'' in 2019 as its phylogenomic resource. See also * PhyloCode * National Center for Biotechnology Informa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Asgardaeota
Asgard or Asgardarchaeota is a proposed superphylum consisting of a group of archaea that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota, and Heimdallarchaeota. It appears the eukaryotes emerged within the Asgard, in a branch containing the Heimdallarchaeota. This supports the two-domain system of classification over the three-domain system. Discovery and nomenclature In the summer of 2010, sediments were analysed from a gravity core taken in the rift valley on the Knipovich ridge in the Arctic Ocean, near the Loki's Castle hydrothermal vent site. Specific sediment horizons previously shown to contain high abundances of novel archaeal lineages were subjected to metagenomic analysis. In 2015, an Uppsala University-led team proposed the Lokiarchaeota phylum based on phylogenetic analyses using a set of highly conserved protein-coding genes. Through a reference to the hydrothermal vent complex from which the first genome sample originated, the name refers to Loki, the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Bacteria also live in symbiotic and parasitic relationsh ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Planctobacteria
The PVC superphylum is a superphylum of bacteria named after its three important members, Planctomycetota, Verrucomicrobiota, and Chlamydiota. Cavalier-Smith postulated that the PVC bacteria probably lost or reduced their peptidoglycan cell wall twice. It has been hypothesised that a member of the PVC clade might have been the host cell in the endosymbiotic event that gave rise to the first proto-eukaryotic cell. Cavalier-Smith calls the same group Planctobacteria and considers it a phylum. However, this is not followed by the larger scientific community. In the Cavalier-Smith bacterial megaclassification, it is within the bacterial Gracilicutes infra-kingdom and comprises the phyla Chlamydiota, Lentisphaerota, Planctomycetota, Verrucomicrobiota. Molecular signatures Planctomycetota, Verrucomicrobiota, and Chlamydiota in the traditional molecular phylogeny view are considered as phyla and also cluster together in the PVC superphylum, along with the candidate phyla Omnitrophic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Terrabacteria
Terrabacteria is a taxon containing approximately two-thirds of prokaryote species, including those in the gram positive phyla (Actinomycetota and Bacillota) as well as the phyla "Cyanobacteria", Chloroflexota, and Deinococcota. It derives its name (''terra'' = "land") from the evolutionary pressures of life on land. Terrabacteria possess important adaptations such as resistance to environmental hazards (e.g., desiccation, ultraviolet radiation, and high salinity) and oxygenic photosynthesis. Also, the unique properties of the cell wall in gram-positive taxa, which likely evolved in response to terrestrial conditions, have contributed toward pathogenicity in many species. These results now leave open the possibility that terrestrial adaptations may have played a larger role in prokaryote evolution than currently understood. Terrabacteria was proposed in 2004 for Actinomycetota, "Cyanobacteria", and Deinococcota and was expanded later to include Bacillota and Chloroflexota. Othe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Methanopyri
In taxonomy, the Methanopyri are a class of the Euryarchaeota.See the NCBI The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...br>webpage on Methanopyri Data extracted from the References Further reading Scientific journals * * Scientific books * * Scientific databases External links Archaea classes Euryarchaeota {{Euryarchaeota-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Methanococci
Methanococci is a class of methanogenic archaea in the phylum Euryarchaeota.See the NCBIbr>webpage on Methanococci Data extracted from the They can be mesophilic, thermophilic or hyperthermophilic A hyperthermophile is an organism that thrives in extremely hot environments—from 60 °C (140 °F) upwards. An optimal temperature for the existence of hyperthermophiles is often above 80 °C (176 °F). Hyperthermophiles are often within the doma .... References Further reading Scientific journals * * * Scientific books * * Scientific databases External links Archaea classes Euryarchaeota {{Euryarchaeota-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Thermococci
In taxonomy, the Thermococci are a class of microbes within the Euryarchaeota.See the NCBIbr>webpage on Thermococci Data extracted from the They live in extremely hot environments, such as hydrothermal vents, and they have optimal growth temperatures above 80 °C. '' Thermococcus'' and ''Pyrococcus'' (literally "balls of fire") are both obligately anaerobic organism, anaerobic chemoorganotrophs. ''Thermococcus'' prefers 70-95 °C and ''Pyrococcus'' 70-100 °C. '' Palaeococcus helgesonii'', recently discovered in the Tyrrhenian Sea, is an aerobic chemoheterotrophic that grows at temperatures of 45-85 °C with an optimal temperature of 80 °C. '' Thermococcus gammatolerans'' sp. nov. was recently discovered in the Guaymas Basin, and it grows at temperatures from 55-95 °C with an optimal temperaturearound 88 °C with an optimal pH of 6. It has pronounced radioresistance and can survive gamma radiation at 30 kGy. See also * List of Archae ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
