'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 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

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 121 (June 2015)^[4][5] and contains all type species with validly published names.

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 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 Thermoflexus hugenholtzii Dehalococcoidaceae Caldilineaceae Ardenticatena maritima Anaerolineaceae Ktedonobacteria Thermomicrobia Chloroflexi Nitrospiraceae Deinococci Thermoanaerobaculum aquaticum Caldithrix Gemmatimonas aurantiaca Fibrobacter Planctobacteria Planctomycetes Phycisphaera mikrensis Planctomycetales Chlamydiales Lentisphaerae Oligosphaera ethanolica Lentisphaeria Verrucomicrobia Opitutae Verrucomicrobiales Sphingobacteria Chlorobi Ignavibacteriaceae Chlorobiaceae Bacteroidetes Thiobacteria Deltaproteobacteria Deferrisoma carnini Desulfovibrionales Desulfurellaceae Epsilonproteobacteria Acidobacteria Holophagae Bryobacter aggregatus Acidobacteriaceae Chrysiogenaceae Deferribacteraceae Spirochaetales Fusobacteriales Elusimicrobium minutum Armatimonadetes Mariprofundus ferrooxydans Rhodobacteria Alphaproteobacteria Chromatibacteria 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. 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. "ARB-SILVA release LTPs 121: overview" (PDF).
5. "ARB-SILVA release LTPs 121: full tree" (PDF).

External links