'The All-Species Living Tree' Project
Multi tool use
'The All-Species Living Tree' Project logo
'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 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
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). This 16S rRNA-based phylogenetic tree is based on the ARB-SILVA release LTPs 121 (June 2015)[4][5] and contains all type species with validly published names.
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Domain Archaea
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Thaumarchaeota
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Crenarchaeota (Thermoprotei)
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Euryarchaeota
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Methanopyrus kandleri
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Methanococcales
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Eurythermea
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Thermococcaceae
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Thermoplasmata
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Neobacteria
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Methanobacteriales
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Archaeoglobaceae
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Halomebacteria
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Methanomicrobia
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Halobacteriaceae
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Domain Bacteria
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Thermotogales
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Thermodesulfobiaceae (Firmicutes)
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Synergistaceae Clostridiales Family XV Incertae Sedis (Firmicutes)
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Caldisericum exile
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Thermodesulfobacteriaceae
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Aquificales
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Firmicutes
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Thermaerobacter
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Caldicellulosiruptor
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Thermoanaerobacteraceae
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Thermanaeromonas toyohensis
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Dictyoglomus
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Thermoanaerobacterales Unnamed clade I (incl. Fervidicola)
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Thermoanaerobacterales Unnamed clade II
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Gelria glutamica
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Clostridiales Family XVIII Incertae Sedis
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Sulfobacillus
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Clostridia s.s. (incl. Thermolithobacter, Negativicutes & Thermoanaerobacterales Unnamed clade III)
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Bacilli (incl. Erysipelotrichia & Mollicutes)
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Actinobacteria
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Chloroflexi
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Thermoflexus hugenholtzii
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Dehalococcoidaceae
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Caldilineaceae
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Ardenticatena maritima
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Anaerolineaceae
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Ktedonobacteria
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Thermomicrobia
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Chloroflexi
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Nitrospiraceae
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Deinococci
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Thermoanaerobaculum aquaticum
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Caldithrix
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Gemmatimonas aurantiaca
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Fibrobacter
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Planctobacteria
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Planctomycetes
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Phycisphaera mikrensis
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Planctomycetales
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Chlamydiales
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Lentisphaerae
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Oligosphaera ethanolica
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Lentisphaeria
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Verrucomicrobia
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Opitutae
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Verrucomicrobiales
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Sphingobacteria
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Chlorobi
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Ignavibacteriaceae
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Chlorobiaceae
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Bacteroidetes
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Thiobacteria
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Deltaproteobacteria
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Deferrisoma carnini
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Desulfovibrionales
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Desulfurellaceae
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Epsilonproteobacteria
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Acidobacteria
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Holophagae
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Bryobacter aggregatus
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Acidobacteriaceae
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Chrysiogenaceae
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Deferribacteraceae
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Spirochaetales
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Fusobacteriales
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Elusimicrobium minutum
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Armatimonadetes
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Mariprofundus ferrooxydans
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Rhodobacteria
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Alphaproteobacteria
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Chromatibacteria
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Gammaproteobacteria (paraphyletic)
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Betaproteobacteria
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References
^ Yarza, P.; Richter, M.; Peplies, J. R.; Euzeby, J.; Amann, R.; Schleifer, K. H.; Ludwig, W.; Glöckner, F. O.; Rosselló-Móra, R. (2008). "The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains". Systematic and Applied Microbiology. 31 (4): 241–250. doi:10.1016/j.syapm.2008.07.001. PMID 18692976.
^ Yarza, Pablo; Ludwig, Wolfgang; Euzéby, Jean; Amann, Rudolf; Schleifer, Karl-Heinz; Glöckner, Frank Oliver; Rosselló-Móra, Ramon (2010). "Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses". Systematic and Applied Microbiology. 33 (6): 291–299. doi:10.1016/j.syapm.2010.08.001. PMID 20817437.
^ Munoz, R. L.; Yarza, P.; Ludwig, W.; Euzéby, J.; Amann, R.; Schleifer, K. H.; Oliver Glöckner, F.; Rosselló-Móra, R. (2011). "Release LTPs104 of the All-Species Living Tree". Systematic and Applied Microbiology. 34 (3): 169–170. doi:10.1016/j.syapm.2011.03.001. PMID 21497273.
^ "ARB-SILVA release LTPs 121: overview" (PDF).
^ "ARB-SILVA release LTPs 121: full tree" (PDF).
External links
Microbiology: Bacteria
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Medical
microbiology | - infection
- Coley's toxins
- Exotoxin
- Lysogenic cycle
- Pathogenic bacteria
- resistance
|
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Biochemistry
and ecology |
Oxygen
preference |
Aerobic
Anaerobic
- Microaerophile
- Nanaerobe
- Aerotolerant
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|---|
| Other | - Extremophile
Human flora
- Gut
- Lung
- Mouth
- Skin
Vaginal (In pregnancy)
- Placental
- Uterine
- Salivary
- Microbial metabolism
- Nitrogen fixation
- Microbial ecology
- Primary nutritional groups
- Substrate preference
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| Shape | - Bacterial cellular morphologies
Coccus
- Bacillus
- Coccobacillus
- Spiral
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| Structure |
Cell
envelope | - Cell membrane
Cell wall: Peptidoglycan
Gram-positive bacteria only: Teichoic acid
- Lipoteichoic acid
- Endospore
Gram-negative bacteria only: Bacterial outer membrane
- Periplasmic space
Mycobacteria only: Arabinogalactan
- Mycolic acid
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Outside
envelope | - Bacterial capsule
- Slime layer
- S-layer
- Glycocalyx
- Pilus
- Fimbria
- Non-motile bacteria
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| Composite | |
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| Taxonomy | - Bacteria (classifications)
- Bacterial phyla
Former groupings: Schizomycetes
- Monera
Prokaryota
- Gracilicutes
- Firmicutes
- Mollicutes
- Mendosicutes
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