'The All-Species Living Tree' Project

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'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[edit]

See also: bacterial phyla

The tree was created by ML 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 111 (February 2013)[4][5] and contains all type species with validly published names.

Domain Archaea

Crenarchaeota (Thermoprotei)


Euryarchaeota

Methanopyrus kandleri




Methanococcales



Eurythermea

Thermococcaceae




Methanomassiliicoccus luminyensis



Thermoplasmatales




Neobacteria

Methanobacteriales




Archaeoglobaceae


Halomebacteria

Methanomicrobia



Halobacteriaceae









Domain Bacteria

Thermotogales




Thermodesulfobiaceae (Firmicutes)




Synergistaceae {Clostridiales Family XV Incertae Sedis} (Firmicutes)




Caldisericum exile





Thermodesulfobacteriaceae



Aquificales




Firmicutes

Thermaerobacter





Caldicellulosiruptor




Thermoanaerobacteraceae




Thermanaeromonas toyohensis




Dictyoglomus



Thermoanaerobacterales Unnamed clade I (incl. Fervidicola)








Thermoanaerobacterales Unnamed clade II





Gelria glutamica




Clostridiales Family XVIII Incertae Sedis



Sulfobacillus






Clostridia s.s. (incl. Thermolithobacter, Negativicutes & Thermoanaerobacterales Unnamed clade III)



Bacilli (incl. Erysipelotrichia & Mollicutes)










Actinobacteria


Chloroflexi


Dehalococcoidaceae




Caldilineaceae



Anaerolineaceae






Ktedonobacteria




Thermomicrobia



Chloroflexi








Nitrospiraceae




Deinococci







Caldithrix




Gemmatimonas aurantiaca



Fibrobacter




Planctobacteria
Planctomycetes

Phycisphaera mikrensis



Planctomycetales





Chlamydiales



Lentisphaerae

Oligosphaera ethanolica



Lentisphaeria



Verrucomicrobia

Opitutae



Verrucomicrobiales







Sphingobacteria
Chlorobi

Ignavibacteriaceae



Chlorobiaceae



Bacteroidetes

Rhodothermaceae [Salinibacteria]




Balneola-Gracilimonas clade




Cytophagales




Sphingobacteriaceae




Saprospiraceae-Chitinophagaceae clade




Cryomorphaceae 1




Flavobacteriales



Bacteroidales












Thiobacteria

Deltaproteobacteria




Deferrisoma carnini




Desulfovibrionales




Desulfurellaceae



Epsilonproteobacteria








Acidobacteria

Holophagae




Bryobacter aggregatus



Acidobacteriaceae







Chrysiogenaceae



Deferribacteraceae





Spirochaetales




Fusobacteriales




Elusimicrobium minutum


Armatimonadetes

Fimbriimonas ginsengisoli




Armatimonas rosea



Chthonomonas calidirosea











Mariprofundus ferrooxydans


Rhodobacteria

Alphaproteobacteria


Chromatibacteria

Gammaproteobacteria (paraphyletic)



Betaproteobacteria

















External links[edit]

References[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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.  edit
  4. ^ "ARB-SILVA release LTPs 115: overview". 
  5. ^ "ARB-SILVA release LTPs 115: full tree".