'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 LTP_12_2021 (Ludwig et al., 2021) (December 2020) and contains all type species with validly published names up to September 2021.[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"

Moorellales {"Moorellia"}

"Calderihabitantales"

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 23 February 2021.
  7. ^ "LTP_all tree in newick format". Retrieved 23 February 2021.
  8. ^ "LTP_12_2021 Release Notes" (PDF). Retrieved 23 February 2021.

External links[]