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All-Species Living Tree Project
'The All-Species Living Tree' Project
'The All-Species Living Tree' Project
is a collaboration between various academic groups/institutes, such as ARB, SILVA rRNA database project, and LPSN, with the aim of assembling a database of 16S rRNA sequences of all validly published species of Bacteria
Bacteria
and Archaea.[1] At one stage, 23S sequences were also collected,[2] but this has since stopped.[3] Currently there are over 10,950 species in the aligned dataset and several more are being added either as new species are discovered or species that are not represented in the database are sequenced. Initially the latter group consisted of 7% of species. Tree[edit] See also: Bacterial phyla The tree was created by maximum likelihood analysis without bootstrap: consequently accuracy is traded off for size and many phylum level clades are not correctly resolved (such as the Firmicutes). (Eukaryotes not present in analysis)
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ARB Project
The ARB Project is a free software package for phylogenetic analysis of rRNA and other biological sequences. Introduction[edit] From the authors' own description,[1]The ARB (from Latin arbor, tree) The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and amino acid sequence data as well. A central database contains processed (aligned) primary structure data. Any additional descriptive data can be stored in database fields assigned to the individual sequences or linked via local or worldwide networks. A phylogenetic tree visualized in the main window can be used for data access and visualization
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Mollicutes
Acholeplasmatales Anaeroplasmatales Entomoplasmatales Haloplasmatales Mycoplasmatales Mollicutes
Mollicutes
is a class of bacteria[6] distinguished by the absence of a cell wall. The word "Mollicutes" is derived from the Latin mollis (meaning "soft" or "pliable"), and cutis (meaning "skin"). Individuals are very small, typically only 0.2–0.3 μm (200-300 nm) in size and have a very small genome size. They vary in form, although most have sterols that make the cell membrane somewhat more rigid. Many are able to move about through gliding, but members of the genus Spiroplasma are helical and move by twisting. The best-known genus in the Mollicutes
Mollicutes
is Mycoplasma. Mollicutes
Mollicutes
are parasites of various animals and plants, living on or in the host's cells
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List Of Prokaryotic Names With Standing In Nomenclature
List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes,[1] following the taxonomy requirements and rulings of the International Code of Nomenclature of Bacteria.[2] The database was curated from 1997 to June 2013 by J. P. Euzéby.[3] From July 2013, LPSN is curated by Aidan C. Parte.[2] Bacterial and Archaeal taxonomy is updated through the journal International Journal of Systematic and Evolutionary Microbiology (IJSB/IJSEM). LPSN is hosted by gandi.net servers located in Baltimore, USA.[4] The site, in addition to keeping track of current taxonomic names, has several reference resources explaining minimal standards for the description of new taxa,[5][3] Latin and Greek grammar aids[6] and lists culture collections worldwide which deal in prokaryotes culture.[7] References[edit]^ Wackett LP (5 June 2014). "Microbial strain collections and information"
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Caldiserica
Caldisericum exile is a species of bacteria sufficiently distinct from other bacteria to be placed in its own family, order, class and phylum.[1] It is the first member of the thermophilic candidate phylum OP5 to be cultured and described. References[edit]^ Koji Mori; Kaoru Yamaguchi; Yayoi Sakiyama; Tetsuro Urabe; Ken-ichiro Suzuki (November 2009). " Caldisericum exile gen. nov., sp. nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiserica phyl. nov., originally called the candidate phylum OP5, and description of Caldisericaceae fam. nov., Caldisericales ord. nov. and Caldisericia classis nov". International Journal of Systematic and Evolutionary Microbiology. 59 (11): 2894–2898. doi:10.1099/ijs.0.010033-0
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Thermanaeromonas Toyohensis
Thermanaeromonas toyohensis is a species of bacteria within the family Thermoanaerobacteraceae. This species is thermophilic, anaerobic, and can reduce thiosulfate. It was originally isolated from a geothermal aquifer more than 500 m below the surface of the Earth.[1] References[edit]^ Mori, K.; S. Hanada; A. Maruyama; K. Marumo (1 September 2002). " Thermanaeromonas toyohensis gen. nov., sp. nov., a novel thermophilic anaerobe isolated from a subterranean vein in the Toyoha Mines". International Journal of Systematic and Evolutionary Microbiology. 52 (5): 1675–1680. doi:10.1099/ijs.0.02201-0
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Dictyoglomus
Dictyoglomus is a genus of bacterium,[3] given its own phylum, called the Dictyoglomi. This organism is extremely thermophilic, meaning it thrives at extremely high temperatures. It is chemoorganotrophic, meaning it derives energy by metabolizing organic molecules. This organism is of interest because it elaborates an enzyme, xylanase, which digests xylan, a heteropolymer of the pentose sugar xylose. By pretreating wood pulp with this enzyme, paper manufacturers can achieve comparable levels of whiteness with much less chlorine bleach. It has been described as Gram-negative, with a triple-layered wall.[4] References[edit]^ J.P. Euzéby. "Dictyoglomi". List of Prokaryotic names with Standing in Nomenclature. Archived from the original on 2011-06-13. Retrieved 2011-06-05.  ^ See the NCBI webpage on Dictyglomi. Data extracted from the "NCBI taxonomy resources"
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Negativicutes
The Negativicutes are a class of firmicute bacteria, whose members have a peculiar cell wall with a lipopolysaccharide outer membrane which stains Gram-negative, unlike most other members of the Firmicutes.[1] Although several neighbouring Clostridia
Clostridia
species (firmicute bacteria) also stain Gram-negative, the proteins responsible for the unusual diderm structure of the Negativicutes may have actually been laterally acquired from Proteobacteria.[1][2][3][4] Additional research is required to confirm the origin of the diderm cell envelope in the Negativicutes. Most members of this class are obligate anaerobes, and occur in habitats such as rivers, lakes, and the intestines of vertebrates. They range from spherical forms, such as Megasphaera and Veillonella, to curved rods, as typified by the selenomonads
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Bacilli
Bacilli
Bacilli
refers to a taxonomic class of bacteria. It includes two orders, Bacillales and Lactobacillales, which contain several well-known pathogens such as Bacillus
Bacillus
anthracis (the cause of anthrax). All Bacilli
Bacilli
are gram-positive bacteria.[1]Contents1 Ambiguity 2 Phylogeny2.1 Bacilli
Bacilli
part 2 (continued)3 ReferencesAmbiguity[edit] Several related concepts make use of similar words, and the ambiguity can create considerable confusion
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Erysipelotrichia
The Erysipelotrichia are a class of bacteria of the phylum Firmicutes. Species of this class are known to be common in the gut microbiome, as they have been isolated from swine manure[1] and increase in composition of the mouse gut microbiome for mice switched to diets high in fat.[2] Phylogeny[edit] The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[3][4] and the phylogeny is based on 16S rRNA-based LTP release 111 by 'The All-Species Living Tree' Project.[5]Aphragmobacteria Haloplasma contractile Antunes et al. 2008 Turicibacter
Turicibacter
sanguinis Bosshard et al. 2002Erysipelotrichaceae 2 Clostridium ramosum (Veillon and Zuber 1898) Holdeman et al. 1971Clostridium saccharogumia Clavel et al. 2007 Clostridium cocleatum Kaneuchi et al. 1979Clostridium spiroforme Kaneuchi et al
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Actinobacteria
The Actinobacteria
Actinobacteria
are a phylum of Gram-positive bacteria. They can be terrestrial or aquatic.[1] They are of great economic importance to humans because agriculture and forests depend on their contributions to soil systems. In soil, they behave much like fungi, helping to decompose the organic matter of dead organisms so the molecules can be taken up anew by plants. In this role the colonies often grow extensive mycelia, like a fungus would, and the name of an important order of the phylum, Actinomycetales
Actinomycetales
(the actinomycetes), reflects that they were long believed to be fungi. Some soil actinobacteria (such as Frankia) live symbiotically with the plants whose roots pervade the soil, fixing nitrogen for the plants in exchange for access to some of the plant's saccharides. Beyond the great interest in Actinobacteria
Actinobacteria
for their soil role, much is yet to be learned about them
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Methanomicrobia
In the taxonomy of microorganisms, the Methanomicrobia
Methanomicrobia
are a class of the Euryarchaeota.[1]Contents1 Phylogeny 2 References 3 Further reading3.1 Scientific journals 3.2 Scientific books 3.3 Scientific databases4 External linksPhylogeny[edit] The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[2] and National Center for Biotechnology Information (NCBI)[3] and the phylogeny is based on 16S rRNA-based LTP release 106 by 'The All-Species Living Tree' Project.[4]? Methanomassiliicoccus luminyensis ♠ Dridi et al. 2011 Methanocella Sakai et al. 2008  Methanosarcinales Methanothrix Huser et al. 1983 Methermicoccus shengliensis
Methermicoccus shengliensis
Cheng et al
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Chloroflexi (phylum)
The Chloroflexi or Chlorobacteria are a phylum of bacteria containing isolates with a diversity of phenotypes including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures, anoxygenic phototrophs, which use light for photosynthesis (green non-sulfur bacteria), and anaerobic halorespirers, which uses halogenated organics (such as the toxic chlorinated ethenes and polychlorinated biphenyls) as electron acceptors. Most bacteria, in terms of diversity, are diderms and stain Gram negative, notable exceptions being Firmicutes
Firmicutes
(low CG Gram positives), Actinobacteria
Actinobacteria
(high CG gram positives) and the Deinococcus–Thermus group (Gram positive, but diderms with thick peptidoglycan)
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Anaerolineaceae
Anaerolinea[5] Bellilinea[5] Brevefilum[5] Candidatus Roseilinea[5] Flexilinea[5] Leptolinea[5] Levilinea[5] Longilinea[5] Ornatilinea[5] Pelolinea[5] Thermanaerothrix[5] Thermomarinilinea[5] Anaerolineaceae is a family of methanogenic bacteria from the order of Anaerolineales.[2][5][6] Anaerolineaceae bacteria occur in marine sediments.[7] References[edit]^ a b c d Satyanarayana, Tulasi; Littlechild, Jennifer; Kawarabayasi, Yutaka (2013). Thermophilic Microbes in Environmental and Industrial Biotechnology: Biotechnology of Thermophiles. Springer Science & Business Media. ISBN 9789400758995.  ^ a b Parker, Charles Thomas; Wigley, Sarah; Garrity, George M; Taylor, Dorothea. "Nomenclature Abstract for Anaerolineaceae Yamada et al. 2006". The NamesforLife Abstracts. doi:10.1601/nm.576.  ^ Parte, A.C. "Anaerolineaceae". www.bacterio.net.  ^ Rada, Elena C. (2015)
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Thermomicrobia
Thermobaculum terrenum Sphaerobacterales ThermomicrobialesThe Thermomicrobia are a group of thermophilic green non-sulfur bacteria. Until 2004, they were classified as a distinct phylum.[1] It has recently been proposed, on the basis of an analysis of genetic affiliations, that the Thermomicrobia should more properly be reclassified as a class belonging to the phylum chloroflexi. The bacteria Sphaerobacter thermophilus originally described as an Actinobacteria is now considered a Thermomicrobia.[2] [3] Taxonomy[4][5][edit] Class ThermomicrobiaGenus Thermobaculum♠ Botero et al. 2004Thermobaculum terrenum♠ Botero et al. 2004Order ThermomicrobialesFamily ThermomicrobiaceaeGenus Thermomicrobium Jackson et al. 1973Thermomicrobium roseum Jackson et al. 1973Order SphaerobacteralesFamily SphaerobacteraceaeGenus Sphaerobacter Demharter et al. 1989Sphaerobacter thermophilus Demharter et al
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Chloroflexi (class)
Herpetosiphonales ChloroflexalesChloroflexineae RoseiflexinaeSynonymsChloroflexia Castenholz 2001The Chloroflexia are one of six classes of bacteria in the phylum Chloroflexi, known as filamentous green non-sulfur bacteria. They produce energy from light and are named for their green pigment, usually found in photosynthetic bodies called chlorosomes. Chloroflexia are typically filamentous, and can move about through bacterial gliding
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