'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]

'The All-Species Living Tree' Project logo

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
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 phylogeny is a summary of the 16S rRNA based LTP_01_2022 and contains all type species with validly published names up to January 2022.[6][7][8]

Domain Archaea
 

Methanopyri

 
 
Crenarchaeida
 

Nitrososphaerota

 
 

Thermoproteota

 
 
Euryarchaeota
 
 
 

Methanococci

 
 

Thermoplasmata

 
 
 
 

"Archaeoglobia"

 
 

Thermococci

 
 
 
 
 

Methanobacteria

 
 
 
 

Methanonatronarchaeia

 
 

Methanomicrobia

 
 
 

Halobacteria

 
 
 
{"Euryarchaeida"}
 
 
Domain Bacteria
"Aquificida"
 

"Thermosulfidibacterota"

 
 

Aquificota

 
 
 
"Synergistetes"
 
 

Caldisericota

 
 

Synergistota

 
 
 
 

Coprothermobacterota

 
 

Thermotogota

 
 
 
 
 

Atribacterota

 
 
 
 

Syntrophorhabdia

 
 
 

Thermotomaculales

 
 

Spirochaetota

 
 
 
 
Firmicutes 3
 
 

Dictyoglomota

 
 

"Caldicellulosiruptorales"

 
 
 
 

"Thermosediminibacteria" [incl. "Ammonificales", DSM-22653]

 
 

"Thermoanaerobacteria" [incl. Thermanaeromonas, Desulfovirgula]

 
 
 
 
"FCB group"
 
 

Fibrobacteria {Fibrobacterota}

 
 

Gemmatimonadota

 
 
 
 

Calditrichota

 
 
 
 

Ignavibacteriota

 
 

Chlorobiota

 
 
 
 

Rhodothermota

 
 
 

Balneolota

 
 

Bacteroidota

 
 
 
 
 
 
 
 
 
Firmicutes 2
 
 

"Sulfobacillia"

 
 

"Thermaerobacteria"

 
 
 
 
 

"Carboxydothermales"

 
 

"Thermacetogeniales"

 
 
 
 

Moorellales {"Moorellia"}

 
 
 
 

"Calderihabitantales"

 
 

"Koleobacterales"

 
 
 
 

Zhaonellaceae

 
 
 

"Desulfitibacterales"

 
 

"Syntrophomonadia"

 
 
 
 
 
 
 
 
 

Gelria

 
 
 

"Symbiobacteriia"

 
 

Actinomycetota

 
 
 
 
 
 

Deinococcota

 
 
 
 

"Melainabacteria"

 
 

"Cyanobacteriota"

 
 
 
 

Armatimonadota

 
 

Chloroflexota

 
 
 
 
 
 
 
 
 
 
 

Nitrospirota

 
 
 

"Thermodesulfobiota"

 
 

Elusimicrobiota

 
 
 
 
 

"Halanaerobiia"

 
 

Acidobacteriota

 
 
 
 
 

Chitinivibrionia

 
"Planctobacteria"
 
 

"Abditibacteriota"

 
 
 

Chlamydiota

 
 
 

Lentisphaerota

 
 
 

Kiritimatiellota

 
 

Verrucomicrobiota

 
 
 
 
 
 

Planctomycetota

 
 
 
 
"Firmicutes" 1
 
 
 
 

Thermolithobacteria

 
 

"Carboxydocellales"

 
 
 
 

"Thermincolia"

 
 

"Desulfofundulaceae"

 
 
 
 
 

UBA4882

 
 

"Selenomonadia"

 
 
 
 
 
 

Limnochordia

 
 

"Desulfotomaculota"

 
 
 
 

"Clostridiia"

 
 
 
 

Fusobacteriota

 
 

Mycoplasmatota

 
 
 

Bacillota

 
 
 
 
 
 
"Hydrobacterida"
 
 
 
 

Thermodesulfobacteriota

 
 
 
 

"Deferrisomatota"

 
 

"Bradymonadia"

 
 
 

Myxococcota

 
 
 
 
 

"Desulfuromonadota"

 
 
 

Bdellovibrionota

 
 

Desulfobacterota

 
 
 
 
 
 

Desulfovibrionia

 
 

Campylobacterota

 
 
 
 
 
 

Chrysiogenota

 
 

Deferribacterota

 
 
 

Pseudomonadota

 
 
 
 
 
 
 
 
 
 
 

See also

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. "The LTP". Retrieved 20 June 2022.
  7. "LTP_all tree in newick format". Retrieved 20 June 2022.
  8. "LTP_01_2022 Release Notes" (PDF). Retrieved 20 June 2022.
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