'The All-Species Living Tree' Project

'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

 
 
 

Methanomassiliicoccus luminyensis

 
 

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. 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. Bibcode:2009Natur.462.1056W. 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.
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