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List of Archaea genera

From Wikipedia, the free encyclopedia

This article lists the genera of the Archaea. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[1] and National Center for Biotechnology Information (NCBI).[2] However, in the List provided below, GTDB has precedence unless otherwise noted.

Phylogeny

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National Center for Biotechnology Information (NCBI) taxonomy was initially used to decorate the genome tree via tax2tree. The 16S rRNA-based Greengenes taxonomy is used to supplement the taxonomy particularly in regions of the tree with no cultured representatives. List of Prokaryotic names with Standing in Nomenclature (LPSN) is used as the primary taxonomic authority for establishing naming priorities. Taxonomic ranks are normalised using phylorank and the taxonomy manually curated to remove polyphyletic groups.[3][4][5][6][7]

Cladogram was taken from the GTDB release 08-RS214 (28th April 2023).[8][9][10] The position of clades with a "question mark" are based on the additional phylogeny of the 16S rRNA-based LTP_12_2021 by The All-Species Living Tree Project.[11][12][13]

Archaea

Phylum "Microcaldota"

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Class "Microcaldia"

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Order "Microcaldales"

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  • Family "Microcaldaceae" Sakai et al. 2022

Phylum "Undinarchaeota"

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Class "Undinarchaeia"

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Order "Undinarchaeales"

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  • Family "Naiadarchaeaceae" Dombrowski et al. 2020
  • Family "Undinarchaeaceae" Dombrowski et al. 2020

Phylum "Altarchaeota"

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Class "Altarchaeia"

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Order "Altarchaeales"

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  • Family "Altarchaeaceae" corrig. Probst et al. 2014

Phylum "Iainarchaeota"

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Class "Iainarchaeia"

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Order "Forterreales"

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  • Family "Forterreaceae" Pallen, Rodriguez-R & Alikhan 2022
    • "Candidatus Forterrea" Probst & Banfield 2017

Order "Iainarchaeales"

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  • Family "Iainarchaeaceae" Rinke et al. 2020

Phylum "Micrarchaeota"

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Phylogeny of Micrarchaeota[8][9][10]
"Norongarragalinales"

"Ca. Norongarragalina"

"Micrarchaeales"
"Micrarchaeaceae"
"Anstonellales"
"Anstonellaceae"

"Ca. Anstonella"

"Bilamarchaeaceae"

"Ca. Bilamarchaeum"

"Fermentimicrarchaeales"

"Ca. Fermentimicrarchaeum"

"Burarchaeales"

"Ca. Burarchaeum"

"Gugararchaeales"

"Ca. Gugararchaeum"

Class "Micrarchaeia"

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Order "Norongarragalinales"

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  • Family "Norongarragalinaceae" Vázquez-Campos et al. 2021

Order "Micrarchaeales"

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  • Family "Micrarchaeaceae" Vázquez-Campos et al. 2021

Order "Anstonellales"

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  • Family "Anstonellaceae" Vázquez-Campos et al. 2021
    • "Candidatus Anstonella" Vázquez-Campos et al. 2021
  • Family "Bilamarchaeaceae" Vázquez-Campos et al. 2021

Order "Fermentimicrarchaeales"

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  • Family "Fermentimicrarchaeaceae" Kadnikov et al. 2020 (Sv326)

Order "Burarchaeales"

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  • Family "Burarchaeaceae" Vázquez-Campos et al. 2021

Order "Gugararchaeales"

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  • Family "Gugararchaeaceae" Vázquez-Campos et al. 2021

Phylum "Huberarchaeaota"

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Class "Huberarchaeia"

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Order "Huberarchaeales"

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  • Family "Huberarchaeaceae" Rinke et al. 2020

Phylum "Aenigmatarchaeota"

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Class "Aenigmatarchaeia"

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Order "Aenigmatarchaeales"

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  • Family "Aenigmatarchaeaceae" corrig. Rinke et al. 2020

Phylum "Nanohalarchaeota"

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Phylogeny of Nanohalobiaceae[8][9][10]

"Candidatus Nanosalinicola"

"Candidatus Nanosalina"

"Candidatus Nanohalobium"

Class "Nanohalarchaeia"

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Order "Nanohalarchaeales"

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  • Family "Nanohalarchaeaceae"

Class "Nanohalobiia"

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Order "Nanohalobiales"

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  • Family "Nanoanaerosalinaceae" Zhao et al. 2022
  • Family "Nanohalalkaliarchaeaceae" La Cono et al. 2020
  • Family "Nanohalobiaceae" La Cono et al. 2020

Phylum "Nanoarchaeota"

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Phylogeny of "Nanoarchaeota"[8][9][10]
"Nanoarchaeia"
"Nanoarchaeales"
"Nanoarchaeaceae"

"Nanoarchaeum"

"Nanopusillaceae"

"Ca. Nanoclepta"

"Ca. Nanopusillus"

"Tiddalikarchaeales"

"Ca. Tiddalikarchaeum"

"Parvarchaeales"

"Ca. Parvarchaeum"

Class "Nanoarchaeia"

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Nanoarchaeia incertae sedis

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Order "Nanoarchaeales"

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  • Family "Nanoarchaeaceae" Huber et al. 2011
  • Family "Nanopusillaceae" Huber et al. 2011
    • Nanobdella Kato et al. 2022
    • "Candidatus Nanoclepta" St. John et al. 2019
    • "Candidatus Nanopusillus" Wurch et al. 2016 ["Candidatus Nanobsidianus" Castelle et al. 2015]

Order "Tiddalikarchaeales"

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  • Family "Tiddalikarchaeaceae" Vázquez-Campos et al. 2021

Order "Parvarchaeales"

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Phylum "Asgardaeota"

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Phylogeny of Asgardaeota[8][9][10]

Asgardaeota incertae sedis

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  • Class "Asgardarchaeia"
    • Order "Asgardarchaeales"
      • Family "Asgardarchaeaceae" Eme et al. 2023
  • Class "Balderarchaeia"
    • Order "Balderarchaeales"
      • Family "Balderarchaeaceae" Xie et al. 2022
  • Class "Freyrarchaeia"
    • Order "Freyrarchaeales"
  • Class "Njordarchaeia"
    • Order "Njordarchaeales"
  • Class "Tyrarchaeia"
    • Order "Tyrarchaeales"
      • Family "Tyrarchaeaceae" Xie et al. 2022

Class "Sifarchaeia"

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Order "Borrarchaeales"

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  • Family "Borrarchaeaceae" Liu et al. 2021

Order "Sifarchaeales"

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  • Family "Sifarchaeaceae" Sun et al. 2021
    • "Candidatus Sifarchaeum" corrig. Farag, Zhao & Biddle 2020

Class "Wukongarchaeia"

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Order "Wukongarchaeales"

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  • Family "Wukongarchaeaceae" Liu et al. 2021

Class "Heimdallarchaeia"

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Order "Hodarchaeales"

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  • Family "Hodarchaeaceae" Liu et al. 2021

Order "Gerdarchaeales"

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Order "Kariarchaeales"

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  • Family "Kariarchaeaceae" Liu et al. 2021

Order "Heimdallarchaeales"

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Class "Jordarchaeia"

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Order "Jordarchaeales"

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  • Family "Jordarchaeaceae" Sun et al. 2021

Class "Baldrarchaeia"

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Order "Baldrarchaeales"

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  • Family "Baldrarchaeaceae" corrig. Liu et al. 2021

Class "Thorarchaeia"

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Order "Thorarchaeales"

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Class "Odinarchaeia"

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Order "Odinarchaeales"

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  • Family "Odinarchaeaceae" Tamarit et al. 2022

Class "Hermodarchaeia"

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Order "Hermodarchaeales"

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  • Family "Hermodarchaeaceae" corrig. Liu et al. 2021

Class "Lokiarchaeia"

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Order "Helarchaeales"

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Order "Sigynarchaeales"

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Order "Lokiarchaeales"

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In GTDB as order CR-4

  • Family "Lokiarchaeaceae" Vanwonterghem et al. 2016
    • ?"Candidatus Lokiarchaeum" corrig. Spang et al. 2015 (MBGB, DSAG)
  • Family "Prometheoarchaeaceae" Pallen, Rodriguez-R & Alikhan 2022[17] ("MK-D1")

Phylum "Thermoproteota"

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Phylogeny of Thermoproteota[8][9][10]

Thermoproteota Incertae sedis

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Class "Korarchaeia"

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Order "Korarchaeales"

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Class "Bathyarchaeia"

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Order "Bathyarchaeales"

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  • Family "Bathyarchaeaceae" Khomyakova et al. 2023

Order "Hecatellales"

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  • Family "Hecatellaceae" Rinke et al. 2020

MCG6

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Class Nitrososphaeria_A

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Order "Caldarchaeales"

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Phylogeny of Nitrososphaeria_A[8][9][10]
"Caldarchaeales"
"Caldarchaeaceae"

"Ca. Calditenuis"

"Wolframiiraptoraceae"
  • Family "Caldarchaeaceae" Rinke et al. 2020

Class Nitrososphaeria

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Nitrososphaeria Incertae sedis

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Order "Geothermarchaeales"

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Order "Conexivisphaerales"

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  • Family "Conexivisphaeraceae" Kato et al. 2021 (THSC Group)

Order Nitrososphaerales

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Phylogeny of Nitrososphaerales[8][9][10]

Class "Culexarchaeia"

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Order "Culexarchaeles"

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  • Family "Culexarchaeaceae" Kohtz et al. 2022 ["Methanomediaceae" Berghuis et al. 2019]
    • ?"Candidatus Culexarchaeum" Kohtz et al. 2022 ["Candidatus Methanomedium" Berghuis et al. 2019]
  • Family "Culexmicrobiaceae" Kohtz et al. 2022

Class "Methanomethylicia"

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Methanomethylicia incertae sedis

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  • Order "Methanohydrogenicales"
    • Family "Methanohydrogenicaceae" Berghuis et al. 2019
  • Order "Methanomethylarchaeales"
    • Family "Methanomethylarchaeceae" corrig. Hua et al. 2019
  • Order "Methanomethylovorales"
    • Family "Methanomethylovoraceae" Hua et al. 2019

Order "Nezhaarchaeales"

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Order "Methanomethylicales"

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  • Family "Candidatus Methanomethylicaceae" corrig. Vanwonterghem et al. 2016

Class Thermoproteia

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Order "Gearchaeales"

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Order Thermofilales

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Order Thermoproteales

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Phylogeny of Thermoproteales[8][9][10]
Thermoproteaceae
"Thermocladiaceae"

Class "Sulfolobia"

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Order "Marsarchaeales"

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Order Sulfolobales

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Phylogeny of Sulfolobales[8][9][10]

Phylum "Hadarchaeota"

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Class "Persephonarchaeia"

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Class "Hadarchaeia"

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Order "Hadarchaeales"

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  • Family "Hadarchaeaceae" Chuvochina et al. 2019 ex Chuvochina et al. 2023

Phylum Methanobacteriota_B

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Phylogeny of Methanobacteriota_B[8][9][10]
Thermococci
"Methanofastidiales"

"Ca. Methanofastidiosum"

"Methanofastidiosaceae"
Thermococcales
Thermococcaceae

Class "Theionarchaeia"

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Class Thermococci

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Order "Methanofastidiosales"

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  • Family "Methanofastidiosaceae" Rinke et al. 2020

Order Thermococcales

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Phylum "Hydrothermarchaeota"

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Class "Hydrothermarchaeia"

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Order "Hydrothermarchaeales"

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  • Family "Hydrothermarchaeaceae" Chuvochina et al. 2019 ex Chuvochina et al. 2023

Phylum "Methanobacteriota"

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Phylogeny of Methanobacteriota[8][9][10]

Class Methanopyri

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Order Methanopyrales

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Class Methanococci

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Order Methanococcales

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Class Methanobacteria

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Order Methanobacteriales

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Phylum "Thermoplasmatota"

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Phylogeny of Thermoplasmatota[8][9][10]

Thermoplasmatota incertae sedis

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Order "Yaplasmatales"

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Class "Izemarchaea"

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Order "Thermoprofundales"

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  • (MBG-D, E2)

Class "Poseidoniia"

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Order MGIII

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Order "Poseidoniales"

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  • Family "Poseidoniaceae" corrig. Rinke et al. 2019
  • Family "Thalassarchaeaceae" corrig. Rinke et al. 2019

Class Thermoplasmata

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Order "Lunaplasmatales"

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  • Family "Lunaplasmataceae" Zinke et al. 2021

Order "Natronoplasmatales"

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Phylogeny of Natronoplasmatales[8][9][10]

"Candidatus Haladaptiplasma"

"Candidatus Natronoplasma"

"Candidatus Saliniplasma"

Order "Proteinoplasmatales"

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  • (SG8-5)

Order "Gimiplasmatales"

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  • Family "Gimiplasmataceae" Hu et al. 2020

Order "Sysuiplasmatales"

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  • Family "Sysuiplasmataceae" Yuan et al. 2021

Order Methanomassiliicoccales

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Phylogeny of Methanomassiliicoccales[8][9][10]
Methanomassiliicoccaceae

Methanomassiliicoccus

Methanomethylophilaceae"

"Candidatus Methanarcanum"

"Candidatus Methanomethylophilus"

"Candidatus Methanogranum"

"Candidatus Methanoplasma"

Order "Aciduliprofundales"

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  • Family "Aciduliprofundaceae" Rinke et al. 2020

Order Thermoplasmatales

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Phylogeny of Thermoplasmatales[8][9][10]

Phylum "Halobacteriota"

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Phylogeny of Halobacteriota[8][9][10]
"Methanoliparia"

"Methanoliparales"

"Syntropharchaeia"

"Syntropharchaeales"

"Methanocellia"

Methanocellales

"Methanosarcinia"
"Methanosarcinia_A"

Methanosarcinales_A

"Methanomicrobia"

Methanomicrobiales

Halobacteriota incertae sedis

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Order "Methanoflorentales"

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  • Family "Methanoflorentaceae" Mondav et al. 2014

Class Archaeoglobi

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Phylogeny of Archaeoglobales[8][9][10]

Order "Mnemosynellales"

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  • Family "Mnemosynellaceae" Adam et al. 2022

Order Archaeoglobales

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Class "Methanoliparia"

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Order "Methanoliparales"

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Class "Syntropharchaeia"

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Order "Methanophagales"

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  • Family ?"Veteromethanophagaceae" Vulcano et al. 2022
  • Family "Methanophagaceae" Chadwick et al. 2022
  • Family "Methanoxibalbaceae" Laso-Pérez et al. 2022

Order "Syntropharchaeales"

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  • Family "Syntropharchaeaceae" corrig. (ANME-2 cluster)

Class "Methanocellia"

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Order Methanocellales

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  • Family Methanocellaceae Sakai et al. 2008

Class "Methanosarcinia"

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Order Methanotrichales

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Order Methanosarcinales

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Phylogeny of Methanosarcinales[8][9][10]

Class Methanosarcinia A

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Order Methanosarcinales_A

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  • Family Methermicoccaceae Cheng et al. 2007

Class Methanomicrobia

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Order "Alkanophagales"

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  • Family "Alkanophagaceae"

Order Methanomicrobiales

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Phylogeny of Methanomicrobiales[8][9][10]

Class "Hikarchaeia"

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Order "Hikarchaeales"

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  • Family "Hikarchaeaceae" Martijn et al. 2020 (MG-IV)

Class "Methanonatronarchaeia"

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Order "Methanonatronarchaeales"

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Class Halobacteria

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Phylogeny of Halobacteria[8][9][10]
Halobacteriales

Order "Halorutilales"

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  • Family "Halorutilaceae" Durán-Viseras et al. 2023

Order Halobacteriales

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Phylogeny of Natrialbaceae[8][9][10]
Phylogeny of Haloferacaceae[8][9][10]

See also

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References

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  1. ^ J.P. Euzéby. "Archaea". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-06-27.
  2. ^ Sayers; et al. "Archaea". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
  3. ^ Parks, DH; Chuvochina, M; Waite, DW; Rinke, C; Skarshewski, A; Chaumeil, PA; Hugenholtz, P (November 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life". Nature Biotechnology. 36 (10): 996–1004. bioRxiv 10.1101/256800. doi:10.1038/nbt.4229. PMID 30148503. S2CID 52093100.
  4. ^ Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv 10.1101/771964. doi:10.1038/s41587-020-0501-8. PMID 32341564. S2CID 216560589.
  5. ^ Chaumeil, PA; Mussig, AJ; Hugenholtz, P; Parks, DH (15 November 2019). "GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database". Bioinformatics. 36 (6): 1925–1927. doi:10.1093/bioinformatics/btz848. PMC 7703759. PMID 31730192.
  6. ^ Almeida, Alexandre; Nayfach, Stephen; Boland, Miguel; Strozzi, Francesco; Beracochea, Martin; Shi, Zhou Jason; Pollard, Katherine S.; Sakharova, Ekaterina; Parks, Donovan H.; Hugenholtz, Philip; Segata, Nicola; Kyrpides, Nikos C.; Finn, Robert D. (20 July 2020). "A unified catalog of 204,938 reference genomes from the human gut microbiome". Nature Biotechnology. 39 (1): 105–114. doi:10.1038/s41587-020-0603-3. PMC 7801254. PMID 32690973.
  7. ^ Nayfach, Stephen; et al. (9 November 2020). "A genomic catalog of Earth's microbiomes". Nature Biotechnology. 39 (4): 499–509. doi:10.1038/s41587-020-0718-6. PMC 8041624. PMID 33169036.
  8. ^ a b c d e f g h i j k l m n o p q r s t u v w "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
  9. ^ a b c d e f g h i j k l m n o p q r s t u v w "ar53_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  10. ^ a b c d e f g h i j k l m n o p q r s t u v w "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
  11. ^ "The LTP". Retrieved 23 February 2021.
  12. ^ "LTP_all tree in newick format". Retrieved 23 February 2021.
  13. ^ "LTP_12_2021 Release Notes" (PDF). Retrieved 23 February 2021.
  14. ^ a b c Ruize Xie, Yinzhao Wang, Danyue Huang, Jialin Hou, Liuyang Li, Haining Hu, Xiaoxiao Zhao, Fengping Wang: Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes. In: Science China Life Sciences, vol. 65, p. 818–829, April 2022. doi:10.1007/s11427-021-1969-6, PMID 34378142. Epub: Aug. 6, 2021. Along with:Njordarchaeota, a new candidate for a sister group to eukaryotes. EurekAlert!, Oct. 20, 2021.
  15. ^ LPSN: Order "Candidatus Freyrarchaeales"
  16. ^ LPSN: Order "Candidatus Njordarchaeales"
  17. ^ a b c Fabai Wu, Daan R. Speth, Alon Philosof, Antoine Crémière, Aditi Narayanan, Roman A. Barco, Stephanie A. Connon, Jan P. Amend, Igor A. Antoshechkin, Victoria J. Orphan: Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes. In: Nature Microbiology volume 7, p. 200–212, Jan 13, 2022. doi:10.1038/s41564-021-01039-y, PMID 35027677, PMC 8813620. See also Extended Data Fig. 2.
  18. ^ LPSN: Family "Candidatus Sigynarchaeaceae"
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