Genome Taxonomy Database
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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 Infor ...
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Australian Centre For Ecogenomics
Australian(s) may refer to: Australia * Australia, a country * Australians, citizens of the Commonwealth of Australia ** European Australians ** Anglo-Celtic Australians, Australians descended principally from British colonists ** Aboriginal Australians, indigenous peoples of Australia as identified and defined within Australian law * Australia (continent) ** Indigenous Australians * Australian English, the dialect of the English language spoken in Australia * Australian Aboriginal languages * ''The Australian'', a newspaper * Australiana, things of Australian origins Other uses * Australian (horse), a racehorse * Australian, British Columbia, an unincorporated community in Canada See also * The Australian (other) * Australia (other) * * * Austrian (other) Austrian may refer to: * Austrians, someone from Austria or of Austrian descent ** Someone who is considered an Austrian citizen, see Austrian nationality law * Austrian German dialect * Somet ...
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Open-source
Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized software development model that encourages open collaboration. A main principle of open-source software development is peer production, with products such as source code, blueprints, and documentation freely available to the public. The open-source movement in software began as a response to the limitations of proprietary code. The model is used for projects such as in open-source appropriate technology, and open-source drug discovery. Open source promotes universal access via an open-source or free license to a product's design or blueprint, and universal redistribution of that design or blueprint. Before the phrase ''open source'' became widely adopted, developers and producers have used a variety of other terms. ''Open source'' ga ...
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SILVA Ribosomal RNA Database
SILVA is a ribosomal RNA database established in collaboration between the Microbial Genomics Group at the Max Planck Institute for Marine Microbiology in Bremen, Germany, the Department of Microbiology at the Technical University Munich, and Ribocon. Release 117 of the database (January 2014) held more than 4,000,000 small subunit (SSU - 16S/18S) and 400,000 large subunit In structural biology, a protein subunit is a polypeptide chain or single protein molecule that assembles (or "''coassembles''") with others to form a protein complex. Large assemblies of proteins such as viruses often use a small number of ... (LSU - 23S/28S) sequences. Sequences are provided as files for the ARB software environment. See also * List of biological databases#RNA databases References {{reflist, refs= Marc P. Hoeppner, Lars E. Barquist, Paul P. Gardner (2014)An Introduction to RNA Databases ''Methods in Molecular Biology'' 1097: 107–123. {{doi, 10.1007/978-1-62703-709-9_6.
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National Center For Biotechnology Information
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 NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper. The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for biomedical literature. Other databases include the NCBI Epigenomics database. All these databases are available online through the Entrez search engine. NCBI was directed by David Lipman, one of the original authors of the BLAST sequence alignment program and a widely respected figure in bioinformatics. GenBank NCBI had responsibility for making available the GenBank DNA seq ...
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PhyloCode
The ''International Code of Phylogenetic Nomenclature'', known as the ''PhyloCode'' for short, is a formal set of rules governing phylogenetic nomenclature. Its current version is specifically designed to regulate the naming of clades, leaving the governance of species names up to the rank-based nomenclature codes ('' ICN'', '' ICNCP'', '' ICNP'', ''ICZN'', '' ICVCN''). The ''PhyloCode'' is associated with the International Society for Phylogenetic Nomenclature (ISPN). The companion volume, ''Phylonyms'', establishes 300 taxon names under ''PhyloCode'', serving as examples for those unfamiliar with the code. RegNum is an associated online database for registered clade names. The ''PhyloCode'' regulates phylogenetic nomenclature by providing rules for deciding which associations of names and definitions are considered established, which of those will be considered homonyms or synonyms, and which one of a set of synonyms or homonyms will be considered accepted (generally the one re ...
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Bergey's Manual Of Systematics Of Archaea And Bacteria
''Bergey's Manual of Systematic Bacteriology'' is the main resource for determining the identity of prokaryotic organisms, emphasizing bacterial species, using every characterizing aspect. The manual was published subsequent to the ''Bergey's Manual of Determinative Bacteriology'', though the latter is still published as a guide for identifying unknown bacteria. First published in 1923 by David Hendricks Bergey, it is used to classify bacteria based on their structural and functional attributes by arranging them into specific familial orders. However, this process has become more empirical in recent years. The ''Taxonomic Outline of Bacteria and Archaea'' is a derived publication indexing taxon names from version two of the manual. It used to be available for free from the Bergey's manual trust website until September 2018. Michigan State University provides an alternative version that indexes NamesforLife records. The five-volume BMSB is officially replaced by ''Bergey's Manual ...
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Metagenomic
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale ...
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Human Gut Microbiome
Gut microbiota, gut microbiome, or gut flora, are the microorganisms, including bacteria, archaea, fungi, and viruses that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut microbiota. The gut is the main location of the human microbiome. The gut microbiota has broad impacts, including effects on colonization, resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, controlling immune function, and even behavior through the gut–brain axis. The microbial composition of the gut microbiota varies across regions of the digestive tract. The colon contains the highest microbial density recorded in any habitat on Earth, representing between 300 and 1000 different species. Bacteria are the largest and to date, best studied component and 99% of gut bacteria come from about 30 or 40 species. Up to 60% of the dry mass of feces is bacteria. Over 99% of the bact ...
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Average Nucleotide Identity
Bacterial genomes are generally smaller and less variant in size among species when compared with genomes of eukaryotes. Bacterial genomes can range in size anywhere from about 130 kbp to over 14 Mbp. A study that included, but was not limited to, 478 bacterial genomes, concluded that as genome size increases, the number of genes increases at a disproportionately slower rate in eukaryotes than in non-eukaryotes. Thus, the proportion of non-coding DNA goes up with genome size more quickly in non-bacteria than in bacteria. This is consistent with the fact that most eukaryotic nuclear DNA is non-gene coding, while the majority of prokaryotic, viral, and organellar genes are coding. Right now, we have genome sequences from 50 different bacterial phyla and 11 different archaeal phyla. Second-generation sequencing has yielded many draft genomes (close to 90% of bacterial genomes in GenBank are currently not complete); third-generation sequencing might eventually yield a complete genome i ...
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University Of Queensland
, mottoeng = By means of knowledge and hard work , established = , endowment = A$224.3 million , budget = A$2.1 billion , type = Public research university , chancellor = Peter Varghese , vice_chancellor = Deborah Terry , city = Brisbane, Queensland, Australia , students = 55,305 (2019) , undergrad = 35,051 (2019) , postgrad = 19,939 (2019) , faculty = 2,854 , campus = Multiple sites , colours = Purple , affiliations = Group of Eight Universitas 21 ASAIHL EdX , website = , logo = Logo of the University of Queensland.svg , coor = The University of Queensland (UQ, or Queensland University) is a public research university located primarily in Brisbane, the capital city of the Australian state of Queensland. Founded in 1909 by the Queensland parliament, UQ is one of the six sandstone universities, an informal designation of the oldest university in each state. As per 2023, The University of Queensland is ranked as 2nd in Australia and 42nd in the world. ...
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Species
In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. Other ways of defining species include their karyotype, DNA sequence, morphology, behaviour or ecological niche. In addition, paleontologists use the concept of the chronospecies since fossil reproduction cannot be examined. The most recent rigorous estimate for the total number of species of eukaryotes is between 8 and 8.7 million. However, only about 14% of these had been described by 2011. All species (except viruses) are given a two-part name, a "binomial". The first part of a binomial is the genus to which the species belongs. The second part is called the specific name or the specific epithet (in botanical nomenclature, also sometimes i ...
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Archaea
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this term has fallen out of use. Archaeal cells have unique properties separating them from the other two domains, Bacteria and Eukaryota. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in a laboratory and have been detected only by their gene sequences in environmental samples. Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat, square cells of '' Haloquadratum walsbyi''. Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes invo ...
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