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'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.

Similar (and more recent) projects include the Genomic Encyclopedia of Bacteria and Archaea (GEBA), which focused on whole genome sequencing of bacteria and archaea.[4][5]

Tree

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) and contains all type species with validly published names up to December 2014.[6][7]

Domain Archaea

Thaumarchaeota

Crenarchaeota (Thermoprotei)

Euryarchaeota

Methanopyrus kandleri

Methanococcales

Eurythermea

Thermococcaceae

Thermoplasmata

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

(incl. )

Sulfobacillus

Clostridia s.s. (incl. , Negativicutes & )

Bacilli (incl. Erysipelotrichia & Mollicutes)

Actinobacteria

Chloroflexi

Ardenticatena maritima

Anaerolineaceae

Thermomicrobia

Chloroflexi

Nitrospiraceae

Deinococci

Caldithrix

Gemmatimonas aurantiaca

Fibrobacter

Planctobacteria
Planctomycetes

Phycisphaera mikrensis

Planctomycetales

Chlamydiales

Lentisphaerae

Verrucomicrobia

Sphingobacteria
Chlorobi

Chlorobiaceae

Bacteroidetes

Deltaproteobacteria

Deferrisoma carnini

Desulfovibrionales

Desulfurellaceae

Epsilonproteobacteria

Acidobacteria

Acidobacteriaceae

Chrysiogenaceae

Deferribacteraceae

Spirochaetales

Fusobacteriales

Elusimicrobium minutum

Armatimonadetes

Mariprofundus ferrooxydans

Alphaproteobacteria

Gammaproteobacteria (paraphyletic)

Betaproteobacteria

References

  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. hdl:10261/103580. 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.
  4. ^ Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos; Pukall, Rüdiger; Dalin, Eileen; Ivanova, Natalia N.; Kunin, Victor; Goodwin, Lynne; Wu, Martin; Tindall, Brian J.; Hooper, Sean D. (December 2009). "A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea". Nature. 462 (7276): 1056–1060. doi:10.1038/nature08656. ISSN 0028-0836. PMC 3073058. PMID 20033048.
  5. ^ Kyrpides, Nikos C.; Hugenholtz, Philip; Eisen, Jonathan A.; Woyke, Tanja; Göker, Markus; Parker, Charles T.; Amann, Rudolf; Beck, Brian J.; Chain, Patrick S. G.; Chun, Jongsik; Colwell, Rita R. (5 August 2014). "Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains". PLoS Biology. 12 (8): e1001920. doi:10.1371/journal.pbio.1001920. ISSN 1545-7885. PMC 4122341. PMID 25093819.
  6. ^ ARB-SILVA release LTPs 121: overview (PDF) (Report). Archived from the original (PDF) on 23 September 2015.
  7. ^ ARB-SILVA release LTPs 121: full tree (PDF) (Report). Archived from the original (PDF) on 23 September 2015.

External links

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