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词条 'The All-Species Living Tree' Project
释义

  1. Tree

  2. References

  3. External links

'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

{{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 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.

{{clade
|label1=Domain Archaea
|1={{clade
|1=Thaumarchaeota
|2={{clade
|1=Crenarchaeota (Thermoprotei)
|label2=Euryarchaeota
|2={{clade
|1=Methanopyrus kandleri
|2={{clade
|1=Methanococcales
|2={{clade
|label1=Eurythermea
|1={{clade
|1=Thermococcaceae
|2=Thermoplasmata
|label2=Neobacteria
|2={{clade
|1=Methanobacteriales
|2={{clade
|1=Archaeoglobaceae
|label2=Halomebacteria
|2={{clade
|1=Methanomicrobia
|2=Halobacteriaceae
                   }}                 }}                }}             }}           }}         }}        }}      }} 

|label2=Domain Bacteria
|2={{clade
|1=Thermotogales
|2={{clade
|1=Thermodesulfobiaceae (Firmicutes)
|2={{clade
|1=Synergistaceae {Clostridiales Family XV Incertae Sedis} (Firmicutes)
|2={{clade
|1=Caldisericum exile
|2={{clade
|1={{clade
|1=Thermodesulfobacteriaceae
|2=Aquificales
|2={{clade
|label1=Firmicutes
|1={{clade
|1=Thermaerobacter
|2={{clade
|1={{clade
|1=Caldicellulosiruptor
|2={{clade
|1=Thermoanaerobacteraceae
|2={{clade
|1=Thermanaeromonas toyohensis
|2={{clade
|1=Dictyoglomus
|2=Thermoanaerobacterales Unnamed clade I (incl. Fervidicola)
                           }}                         }}                       }}                     }}

|2={{clade
|1=Thermoanaerobacterales Unnamed clade II
|2={{clade
|1={{clade
|1=Gelria glutamica
|2={{clade
|1=Clostridiales Family XVIII Incertae Sedis
|2=Sulfobacillus
                           }}                         }}

|2={{clade
|1=Clostridia s.s. (incl. Thermolithobacter, Negativicutes & Thermoanaerobacterales Unnamed clade III)
|2=Bacilli (incl. Erysipelotrichia & Mollicutes)
                         }}                       }}                     }}                   }}                 }}

|2={{clade
|1={{clade
|1=Actinobacteria
|label2=Chloroflexi
|2={{clade
|1={{clade
|1={{clade
|1=Thermoflexus hugenholtzii
|2=Dehalococcoidaceae
|2={{clade
|1=Caldilineaceae
|2={{clade
|1=Ardenticatena maritima
|2=Anaerolineaceae
                           }}                         }}                       }}

|2={{clade
|1=Ktedonobacteria
|2={{clade
|1=Thermomicrobia
|2=Chloroflexi
                         }}                       }}                     }}                   }}

|2={{clade
|1=Nitrospiraceae
|2={{clade
|1=Deinococci
|2={{clade
|1=Thermoanaerobaculum aquaticum
|2={{clade
|1={{clade
|1={{clade
|1={{clade
|1=Caldithrix
|2={{clade
|1=Gemmatimonas aurantiaca
|2=Fibrobacter
                                 }}                               }}

|label2=Planctobacteria
|2={{clade
|label1=Planctomycetes
|1={{clade
|1=Phycisphaera mikrensis
|2=Planctomycetales
|2={{clade
|1=Chlamydiales
|2={{clade
|label1=Lentisphaerae
|1={{clade
|1=Oligosphaera ethanolica
|2=Lentisphaeria
|label2=Verrucomicrobia
|2={{clade
|1=Opitutae
|2=Verrucomicrobiales
                                     }}                                   }}                                 }}                               }}                             }}

|label2=Sphingobacteria
|2={{clade
|label1=Chlorobi
|1={{clade
|1=Ignavibacteriaceae
|2=Chlorobiaceae
|2=Bacteroidetes
                             }}                           }}

|2={{clade
|label1=Thiobacteria
|1={{clade
|1=Deltaproteobacteria
|2={{clade
|1=Deferrisoma carnini
|2={{clade
|1=Desulfovibrionales
|2={{clade
|1=Desulfurellaceae
|2=Epsilonproteobacteria
                                   }}                                 }}                               }}                             }}

|2={{clade
|1={{clade
|label1=Acidobacteria
|1={{clade
|1=Holophagae
|2={{clade
|1=Bryobacter aggregatus
|2=Acidobacteriaceae
                                   }}                                 }}

|2={{clade
|1={{clade
|1=Chrysiogenaceae
|2=Deferribacteraceae
|2={{clade
|1=Spirochaetales
|2={{clade
|1=Fusobacteriales
|2={{clade
|1=Elusimicrobium minutum
|2=Armatimonadetes
                                       }}                                     }}                                   }}                                 }}                               }}

|2={{clade
|1=Mariprofundus ferrooxydans
|label2=Rhodobacteria
|2={{clade
|1=Alphaproteobacteria
|label2=Chromatibacteria
|2={{clade
|1=Gammaproteobacteria (paraphyletic)
|2=Betaproteobacteria
                                   }}                                 }}                               }}                             }}                           }}                         }}                       }}                     }}                   }}                 }}               }}             }}           }}         }}       }}     }}   }}

References

1. ^{{Cite journal| last1 = Yarza | first1 = P.| last2 = Richter | first2 = M.| last3 = Peplies | first3 = J. R.| last4 = Euzeby | first4 = J.| last5 = Amann | first5 = R.| last6 = Schleifer | first6 = K. H.| last7 = Ludwig | first7 = W.| last8 = Glöckner | first8 = F. O.| last9 = Rosselló-Móra | first9 = R.| doi = 10.1016/j.syapm.2008.07.001| title = The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains| journal = Systematic and Applied Microbiology| volume = 31| issue = 4| pages = 241–250| year = 2008| pmid = 18692976| pmc =}}
2. ^{{Cite journal | last1 = Yarza | first1 = Pablo | last2 = Ludwig | first2 = Wolfgang | last3 = Euzéby | first3 = Jean | last4 = Amann | first4 = Rudolf | last5 = Schleifer | first5 = Karl-Heinz | last6 = Glöckner | first6 = Frank Oliver | last7 = Rosselló-Móra | first7 = Ramon | title = Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses | journal = Systematic and Applied Microbiology | volume = 33 | issue = 6 | pages = 291–299 | year = 2010 | pmid = 20817437 | doi = 10.1016/j.syapm.2010.08.001}}
3. ^{{Cite journal | last1 = Munoz | first1 = R. L. | last2 = Yarza | first2 = P. | last3 = Ludwig | first3 = W. | last4 = Euzéby | first4 = J. | last5 = Amann | first5 = R. | last6 = Schleifer | first6 = K. H. | last7 = Oliver Glöckner | first7 = F. | last8 = Rosselló-Móra | first8 = R. | doi = 10.1016/j.syapm.2011.03.001 | title = Release LTPs104 of the All-Species Living Tree | journal = Systematic and Applied Microbiology | volume = 34 | issue = 3 | pages = 169–170 | year = 2011 | pmid = 21497273| pmc = }}
4. ^{{Cite journal| title = ARB-SILVA release LTPs 121: overview| url=http://www.arb-silva.de/fileadmin/silva_databases/living_tree/LTP_release_121/LTPs121_SSU_tree_overview.pdf}}
5. ^{{Cite journal| title = ARB-SILVA release LTPs 121: full tree| url=http://www.arb-silva.de/fileadmin/silva_databases/living_tree/LTP_release_121/LTPs121_SSU_tree.pdf}}

External links

  •  
{{Bacteria classification}}{{Bacteria}}{{Use dmy dates|date=January 2011}}{{DEFAULTSORT:All-Species Living Tree Project}}

5 : Bacteria|Bacteriology|Microbiology|Taxonomy (biology)|Systems of bacterial taxonomy

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