Editing Methanogen (section)

== Taxonomy ==

Initially, methanogens were considered to be bacteria, as it was not possible to distinguish archaea and bacteria before the introduction of molecular techniques such as DNA sequencing and PCR. Since the introduction of the domain Archaea by Carl Woese in 1977,<ref>{{Cite journal |last1=Woese |first1=Carl R. |last2=Fox |first2=George E. |date=November 1977 |title=Phylogenetic structure of the prokaryotic domain: The primary kingdoms |journal=Proceedings of the National Academy of Sciences |volume=74 |issue=11 |pages=5088–5090 |doi=10.1073/pnas.74.11.5088 |doi-access=free |pmc=432104 |pmid=270744|bibcode=1977PNAS...74.5088W }}</ref> methanogens were for a prolonged period considered a monophyletic group, later named Euryarchaeota (super)phylum. However, intensive studies of various environments have proved that there are more and more non-methanogenic lineages among methanogenic ones.

The development of genome sequencing directly from environmental samples (metagenomics) allowed the discovery of the first methanogens outside the Euryarchaeota superphylum. The first such putative methanogenic lineage was Bathyarchaeia,<ref>{{Cite journal |last1=Evans |first1=Paul N. |last2=Parks |first2=Donovan H. |last3=Chadwick |first3=Grayson L. |last4=Robbins |first4=Steven J. |last5=Orphan |first5=Victoria J. |last6=Golding |first6=Suzanne D. |last7=Tyson |first7=Gene W. |date=2015-10-23 |title=Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics |url=https://www.science.org/doi/10.1126/science.aac7745 |journal=Science |volume=350 |issue=6259 |pages=434–438 |doi=10.1126/science.aac7745 |pmid=26494757 |bibcode=2015Sci...350..434E |issn=0036-8075}}</ref> a class within the Thermoproteota phylum. Later, it was shown that this lineage is not methanogenic but alkane-oxidizing utilizing highly divergent enzyme Acr similar to the hallmark gene of methanogenesis, methyl-CoM reductase (McrABG).<ref>{{Cite journal |last1=Qi |first1=Yan-Ling |last2=Evans |first2=Paul N. |last3=Li |first3=Yu-Xian |last4=Rao |first4=Yang-Zhi |last5=Qu |first5=Yan-Ni |last6=Tan |first6=Sha |last7=Jiao |first7=Jian-Yu |last8=Chen |first8=Ya-Ting |last9=Hedlund |first9=Brian P. |last10=Shu |first10=Wen-Sheng |last11=Hua |first11=Zheng-Shuang |last12=Li |first12=Wen-Jun |date=2021-08-31 |title=Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in ''Candidatus'' Bathyarchaeia" |url=http://dx.doi.org/10.1128/msystems.00252-21 |journal=mSystems |volume=6 |issue=4 |pages=e0025221 |doi=10.1128/msystems.00252-21 |pmid=34282939 |pmc=8407382 |issn=2379-5077}}</ref> The first isolate of Bathyarchaeum tardum from sediment of coastal lake in Russia showed that it metabolizes aromatic compounds and proteins<ref>{{Cite journal |last1=Khomyakova |first1=Maria A. |last2=Merkel |first2=Alexander Y. |last3=Mamiy |first3=Dana D. |last4=Klyukina |first4=Alexandra A. |last5=Slobodkin |first5=Alexander I. |date=2023-08-22 |title=Phenotypic and genomic characterization of Bathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal class Bathyarchaeia |journal=Frontiers in Microbiology |volume=14 |doi=10.3389/fmicb.2023.1214631 |doi-access=free |issn=1664-302X |pmc=10477458 |pmid=37675420}}</ref> as it was previously predicted based on metagenomic studies.<ref>{{Cite journal |last1=Zhou |first1=Zhichao |last2=Pan |first2=Jie |last3=Wang |first3=Fengping |last4=Gu |first4=Ji-Dong |last5=Li |first5=Meng |date=2018-09-01 |title=Bathyarchaeota: globally distributed metabolic generalists in anoxic environments |url=https://academic.oup.com/femsre/article/42/5/639/5000165 |journal=FEMS Microbiology Reviews |volume=42 |issue=5 |pages=639–655 |doi=10.1093/femsre/fuy023 |pmid=29790926 |issn=1574-6976}}</ref><ref>{{Cite journal |last1=Yu |first1=Tiantian |last2=Wu |first2=Weichao |last3=Liang |first3=Wenyue |last4=Lever |first4=Mark Alexander |last5=Hinrichs |first5=Kai-Uwe |last6=Wang |first6=Fengping |date=2018-06-05 |title=Growth of sedimentary Bathyarchaeota on lignin as an energy source |journal=Proceedings of the National Academy of Sciences |language=en |volume=115 |issue=23 |pages=6022–6027 |doi=10.1073/pnas.1718854115 |doi-access=free |issn=0027-8424 |pmc=6003339 |pmid=29773709|bibcode=2018PNAS..115.6022Y }}</ref><ref>{{Cite journal |last1=Yu |first1=Tiantian |last2=Hu |first2=Haining |last3=Zeng |first3=Xianhong |last4=Wang |first4=Yinzhao |last5=Pan |first5=Donald |last6=Deng |first6=Longhui |last7=Liang |first7=Lewen |last8=Hou |first8=Jialin |last9=Wang |first9=Fengping |date=September 2023 |title=Widespread Bathyarchaeia encode a novel methyltransferase utilizing lignin-derived aromatics |journal=mLife |volume=2 |issue=3 |pages=272–282 |doi=10.1002/mlf2.12082 |issn=2097-1699 |pmc=10989822 |pmid=38817817}}</ref> However, more new putative methanogens outside of Euryarchaeota were discovered based on the presence McrABG.

For instance, methanogens were found in the phyla Thermoproteota (orders Methanomethyliales, Korarchaeales, Methanohydrogenales, Nezhaarchaeales) and Methanobacteriota_B (order Methanofastidiosales). Additionally, some new lineages of methanogens were isolated in pure culture, which allowed the discovery of a new type of methanogenesis: H<sub>2</sub>-dependent methyl-reducing methanogenesis, which is independent of the Wood-Ljungdahl pathway. For example, in 2012, the order Methanoplasmatales from the phylum Thermoplasmatota was described as a seventh order of methanogens.<ref>{{Cite journal |last1=Paul |first1=Kristina |last2=Nonoh |first2=James O. |last3=Mikulski |first3=Lena |last4=Brune |first4=Andreas |date=December 2012 |title="Methanoplasmatales," Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens |url=http://dx.doi.org/10.1128/aem.02193-12 |journal=Applied and Environmental Microbiology |volume=78 |issue=23 |pages=8245–8253 |doi=10.1128/aem.02193-12 |pmid=23001661 |pmc=3497382 |bibcode=2012ApEnM..78.8245P |issn=0099-2240}}</ref> Later, the order was renamed Methanomassiliicoccales based on the isolated from human gut ''Methanomassiliicoccus luminyensis''.<ref>{{Cite journal |last1=Dridi |first1=Bédis |last2=Fardeau |first2=Marie-Laure |last3=Ollivier |first3=Bernard |last4=Raoult |first4=Didier |last5=Drancourt |first5=Michel |date=2012-08-01 |title=Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces |url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.033712-0 |journal=International Journal of Systematic and Evolutionary Microbiology |language=en |volume=62 |issue=Pt_8 |pages=1902–1907 |doi=10.1099/ijs.0.033712-0 |pmid=22859731 |issn=1466-5026|url-access=subscription }}</ref><ref>{{Cite journal |last1=Iino |first1=Takao |last2=Tamaki |first2=Hideyuki |last3=Tamazawa |first3=Satoshi |last4=Ueno |first4=Yoshiyuki |last5=Ohkuma |first5=Moriya |last6=Suzuki |first6=Ken-ichiro |last7=Igarashi |first7=Yasuo |last8=Haruta |first8=Shin |date=2013 |title=Candidatus Methanogranum caenicola: a Novel Methanogen from the Anaerobic Digested Sludge, and Proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a Methanogenic Lineage of the Class Thermoplasmata |url=https://www.jstage.jst.go.jp/article/jsme2/28/2/28_ME12189/_article |journal=Microbes and Environments |language=en |volume=28 |issue=2 |pages=244–250 |doi=10.1264/jsme2.ME12189 |pmc=4070666 |pmid=23524372}}</ref>

Another new lineage in the Halobacteriota phylum, order Methanonatronarchaeales, was discovered in alkaline saline lakes in Siberia in 2017.<ref>{{Cite journal |last1=Sorokin |first1=Dimitry Y. |last2=Merkel |first2=Alexander Y. |last3=Abbas |first3=Ben |last4=Makarova |first4=Kira S. |last5=Rijpstra |first5=W. Irene C. |last6=Koenen |first6=M. |last7=Sinninghe Damsté |first7=Jaap S. |last8=Galinski |first8=Erwin A. |last9=Koonin |first9=Eugene V. |last10=van Loosdrecht |first10=Mark C. M. |date=2018-07-01 |title=Methanonatronarchaeum thermophilum gen. nov., sp. nov. and 'Candidatus Methanohalarchaeum thermophilum', extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov. |journal=International Journal of Systematic and Evolutionary Microbiology |language=en |volume=68 |issue=7 |pages=2199–2208 |doi=10.1099/ijsem.0.002810 |issn=1466-5026 |pmc=6978985 |pmid=29781801}}</ref><ref>{{Cite journal |last1=Sorokin |first1=Dimitry Y. |last2=Makarova |first2=Kira S. |last3=Abbas |first3=Ben |last4=Ferrer |first4=Manuel |last5=Golyshin |first5=Peter N. |last6=Galinski |first6=Erwin A. |last7=Ciordia |first7=Sergio |last8=Mena |first8=María Carmen |last9=Merkel |first9=Alexander Y. |last10=Wolf |first10=Yuri I. |last11=van Loosdrecht |first11=Mark C. M. |last12=Koonin |first12=Eugene V. |date=2017-05-30 |title=Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis |journal=Nature Microbiology |language=en |volume=2 |issue=8 |page=17081 |doi=10.1038/nmicrobiol.2017.81 |pmc=5494993 |pmid=28555626}}</ref> It also employs H<sub>2</sub>-dependent methyl-reducing methanogenesis but intriguingly harbors almost the full Wood-Ljungdahl pathway. However, it is disconnected from McrABG as no MtrA-H complex was detected.<ref>{{Cite journal |last1=Sorokin |first1=Dimitry Y. |last2=Merkel |first2=Alexander Y. |last3=Abbas |first3=Ben |date=November 2022 |title=Ecology of Methanonatronarchaeia |journal=Environmental Microbiology |language=en |volume=24 |issue=11 |pages=5217–5229 |doi=10.1111/1462-2920.16108 |issn=1462-2912 |pmc=9796771 |pmid=35726892|bibcode=2022EnvMi..24.5217S }}</ref><ref>{{Cite journal |last1=Steiniger |first1=Fabian |last2=Sorokin |first2=Dimitry Y. |last3=Deppenmeier |first3=Uwe |date=January 2022 |title=Process of energy conservation in the extremely haloalkaliphilic methyl-reducing methanogen Methanonatronarchaeum thermophilum |url=https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.16165 |journal=The FEBS Journal |language=en |volume=289 |issue=2 |pages=549–563 |doi=10.1111/febs.16165 |pmid=34435454}}</ref>

The [[Taxonomy (biology)|taxonomy]] of methanogens reflects the evolution of these [[archaea]], with some studies suggesting that the Last Archaeal Common Ancestor was methanogenic.<ref>{{Cite journal |last1=Mei |first1=Ran |last2=Kaneko |first2=Masanori |last3=Imachi |first3=Hiroyuki |last4=Nobu |first4=Masaru K |date=2023-02-03 |editor-last=Ma |editor-first=Li-Jun |title=The origin and evolution of methanogenesis and Archaea are intertwined |url=https://academic.oup.com/pnasnexus/article/doi/10.1093/pnasnexus/pgad023/7010768 |journal=PNAS Nexus |volume=2 |issue=2 |pages=pgad023 |doi=10.1093/pnasnexus/pgad023 |issn=2752-6542 |pmc=9982363 |pmid=36874274}}</ref> If correct, this suggests that many archaeal lineages lost the ability to produce methane and switched to other types of metabolism. Currently, most of the isolated methanogens belong to one of three archaeal phyla ([[List of Archaea genera|classification]] GTDB release 220): Halobacteriota, Methanobacteriota, and Thermoplasmatota. Under the International Code of Nomenclature for Prokaryotes,<ref>{{Cite journal |last1=Oren |first1=Aharon |last2=Arahal |first2=David R. |last3=Göker |first3=Markus |last4=Moore |first4=Edward R. B. |last5=Rossello-Mora |first5=Ramon |last6=Sutcliffe |first6=Iain C. |date=2023-05-01 |title=International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision) |url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005585 |journal=International Journal of Systematic and Evolutionary Microbiology |language=en |volume=73 |issue=5a |doi=10.1099/ijsem.0.005585 |pmid=37219928 |issn=1466-5026|hdl=10261/338243 |hdl-access=free }}</ref> all three phyla belong to the same kingdom, Methanobacteriati.<ref>{{Cite web |title=Phylum: Methanobacteriota |url=https://lpsn.dsmz.de/phylum/methanobacteriota |access-date=2024-07-16 |website=lpsn.dsmz.de}}</ref><ref>{{Cite journal |last1=Göker |first1=Markus |last2=Oren |first2=Aharon |date=2024-01-22 |title=Valid publication of names of two domains and seven kingdoms of prokaryotes |url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.006242 |journal=International Journal of Systematic and Evolutionary Microbiology |volume=74 |issue=1 |doi=10.1099/ijsem.0.006242 |pmid=38252124|url-access=subscription }}</ref> In total, more than 150 methanogen species are known in culture, with some represented by more than one [[Strain (biology)|strain]].<ref>{{Cite web |title=Leibniz Institute DSMZ: Welcome to the Leibniz Institute DSMZ |url=https://www.dsmz.de/ |access-date=2024-07-16 |website=www.dsmz.de}}</ref>
* Phylum Halobacteriota
** Class Methanocellia
*** Order Methanocellales
**** Family Methanocellaceae
***** Genus ''Methanocella'' Sakai et al. 2008
******  ''Methanocella paludicola'' Sakai ''et al.'' 2008 (type species)
******  ''Methanocella arvoryzae'' Sakai ''et al.'' 2010
******  ''Methanocella conradii'' Lü and Lu 2012
** Class Methanomicrobia
*** Order [[Methanomicrobiales]]=
**** Family [[Methanocalculaceae]] Zhilina ''et al.'' 2014
**** Family [[Methanocorpusculaceae]] Zellner ''et al.'' 1989
******  ''[[Methanocorpusculum]]'' Zellner ''et al.'' 1988
******  ''Methanocorpusculum parvum'' Zellner ''et al.'' 1988 (type species)
******  ''Methanocorpusculum bavaricum'' Zellner ''et al.'' 1989
******  ''[[Methanocorpusculum labreanum]]''
******  ''Methanocorpusculum sinense'' Zellner ''et al.'' 1989
**** Family [[Methanomicrobiaceae]] Balch and Wolfe 1981==
***** Genus ''[[Methanomicrobium]]'' Balch and Wolfe 1981
****** ''[[Methanomicrobium mobile]]'' (Paynter and Hungate 1968) Balch and Wolfe 1981 (type species)
****** ''Methanomicrobium antiquum'' Mochimaru ''et al.'' 2016
***** Genus ''[[Methanoculleus]]'' Maestrojuán ''et al.'' 1990
****** ''[[Methanoculleus bourgensis]]'' corrig. (Ollivier ''et al.'' 1986) Maestrojuán ''et al.'' 1990 (type species)
****** ''Methanoculleus chikugoensis'' Dianou ''et al.'' 2001
****** ''Methanoculleus horonobensis'' Shimizu ''et al.'' 2013
****** ''Methanoculleus hydrogenitrophicus'' Tian ''et al.'' 2010
****** ''[[Methanoculleus marisnigri]]''
****** ''Methanoculleus palmolei'' Zellner ''et al.'' 1998
****** ''Methanoculleus receptaculi'' Cheng ''et al.'' 2008
****** ''Methanoculleus sediminis'' Chen ''et al.'' 2015
****** ''Methanoculleus submarinus'' Mikucki ''et al.'' 2003
****** ''Methanoculleus taiwanensis'' Weng ''et al.'' 2015
****** ''Methanoculleus thermophilus'' corrig. (Rivard and Smith 1982) Maestrojuán ''et al.'' 1990
***** Genus''[[Methanogenium]]'' Romesser ''et al.'' 1981
****** ''[[Methanogenium cariaci]]'' Romesser ''et al.'' 1981 (type species)
****** ''[[Methanogenium frigidum]]''
****** ''Methanogenium marinum'' Chong ''et al.'' 2003
****** ''[[Methanogenium organophilum]]''
***** Genus''[[Methanofollis]]'' Zellner ''et al.'' 1999
****** ''Methanofollis tationis'' (Zabel ''et al.'' 1986) Zellner ''et al.'' 1999 (type strains)
****** ''Methanofollis aquaemaris'' Lai and Chen 2001
****** ''Methanofollis ethanolicus'' Imachi ''et al.'' 2009
****** ''Methanofollis fontis'' Chen ''et al.'' 2020
****** ''Methanofollis formosanus'' Wu ''et al.'' 2005
****** ''[[Methanofollis liminatans]]'' (Zellner ''et al.'' 1990) Zellner ''et al.'' 1999
**** Family [[Methanoregulaceae]] Sakai ''et al.'' 2012
***** Genus''[[Methanoregula]]'' Bräuer ''et al.'' 2011
****** ''[[Methanoregula boonei]]'' Bräuer ''et al.'' 2011 (type species)
****** ''Methanoregula formicica'' Yashiro ''et al.'' 2011
**** Family [[Methanospirillaceae]] Boone ''et al.'' 2002
****** ''[[Methanospirillum]]'' Ferry ''et al.'' 1974
****** ''[[Methanospirillum hungatei]]'' corrig. Ferry ''et al.'' 1974 (type species)
****** ''Methanospirillum lacunae'' Iino ''et al.'' 2010
****** ''Methanospirillum psychrodurum'' Zhou ''et al.'' 2014
****** ''Methanospirillum stamsii'' Parshina ''et al.'' 2014
** Class [[Methanonatronarchaeia]]
*** Order [[Methanonatronarchaeales]]
**** Family [[Methanonatronarchaeaceae]] Sorokin ''et al.'' 2018
***** Genus''[[Methanonatronarchaeum]]'' Sorokin ''et al.'' 2018
****** ''[[Methanonatronarchaeum thermophilum]]'' Sorokin ''et al.'' 2018 (type species)
** Class Methanosarcinia
*** Order [[Methanosarcinales]]
**** Family [[Methanosarcinaceae]]
***** Genus''[[Methanosarcina]]'' Kluyver and van Niel 1936
****** ''[[Methanosarcina barkeri]]'' Schnellen 1947 (type species)
****** ''[[Methanosarcina acetivorans]]''
****** ''Methanosarcina baltica'' von Klein ''et al.'' 2002
****** ''Methanosarcina flavescens'' Kern ''et al.'' 2016
****** ''Methanosarcina horonobensis'' Shimizu ''et al.'' 2011
****** ''Methanosarcina lacustris'' Simankova ''et al.'' 2002
****** ''[[Methanosarcina mazei]]'' (Barker 1936) Mah and Kuhn 1984
****** ''Methanosarcina semesiae'' Lyimo ''et al.'' 2000
****** ''Methanosarcina siciliae'' (Stetter and König 1989) Ni ''et al.'' 1994
****** ''Methanosarcina soligelidi'' Wagner ''et al.'' 2013
****** ''Methanosarcina spelaei'' Ganzert ''et al.'' 2014
****** ''Methanosarcina subterranea'' Shimizu ''et al.'' 2015
****** ''Methanosarcina thermophila'' Zinder ''et al.'' 1985
****** ''Methanosarcina vacuolata'' Zhilina and Zavarzin 1987
***** Genus''[[Methanimicrococcus]]'' corrig. Sprenger ''et al.'' 2000
****** ''[[Methanimicrococcus blatticola]]'' corrig. Sprenger ''et al.'' 2000
***** Genus''[[Methanococcoides]]'' Sowers and Ferry 1985
****** ''[[Methanococcoides methylutens]]'' Sowers and Ferry 1985 (type species)
****** ''Methanococcoides alaskense'' Singh ''et al.'' 2005
****** ''[[Methanococcoides burtonii]]'' Franzmann ''et al.'' 1993
****** ''Methanococcoides orientis'' Liang ''et al.'' 2022
****** ''Methanococcoides vulcani'' L'Haridon ''et al.'' 2014
***** Genus''[[Methanohalobium]]'' Zhilina and Zavarzin 1988
****** ''[[Methanohalobium evestigatum]]'' corrig. Zhilina and Zavarzin 1988 (type species)
***** Genus''[[Methanohalophilus]]'' Paterek and Smith 1988
****** ''[[Methanohalophilus mahii]]'' Paterek and Smith 1988 (type species)
****** ''Methanohalophilus halophilus'' (Zhilina 1984) Wilharm ''et al.'' 1991
****** ''Methanohalophilus levihalophilus'' Katayama ''et al.'' 2014
****** ''Methanohalophilus portucalensis'' Boone ''et al.'' 1993
****** ''Methanohalophilus profundi'' L'Haridon ''et al.'' 2021
***** Genus''[[Methanolobus]]'' König and Stetter 1983
****** ''[[Methanolobus tindarius]]'' König and Stetter 1983 (type species)
****** ''[[Methanolobus bombayensis]]'' Kadam ''et al.'' 1994
****** ''Methanolobus chelungpuianus'' Wu and Lai 2015
****** ''Methanolobus halotolerans'' Shen ''et al.'' 2020
****** ''Methanolobus mangrovi'' Zhou ''et al.'' 2023
****** ''Methanolobus oregonensis'' (Liu ''et al.'' 1990) Boone 2002
****** ''Methanolobus profundi'' Mochimaru ''et al.'' 2009
****** ''Methanolobus psychrotolerans'' Chen ''et al.'' 2018
****** ''Methanolobus sediminis'' Zhou ''et al.'' 2023
****** ''Methanolobus taylorii'' Oremland and Boone 1994
****** ''Methanolobus vulcani'' Stetter ''et al.'' 1989
****** ''Methanolobus zinderi'' Doerfert ''et al.'' 2009
***** Genus''[[Methanomethylovorans]]'' Lomans ''et al.'' 2004
****** ''[[Methanomethylovorans hollandica]]'' Lomans ''et al.'' 2004 (type species)
****** ''Methanomethylovorans thermophila'' Jiang ''et al.'' 2005
****** ''Methanomethylovorans uponensis'' Cha ''et al.'' 2014
***** Genus''[[Methanosalsum]]'' Boone and Baker 2002
****** ''Methanosalsum zhilinae'' (Mathrani ''et al.'' 1988) Boone and Baker 2002 (type species)
****** ''Methanosalsum natronophilum'' Sorokin ''et al.'' 2015
**** Family [[Methanotrichaceae]]
***** Genus''[[Methanothrix]]'' Huser ''et al.'' 1983
****** ''[[Methanothrix soehngenii]]'' Huser ''et al.'' 1983 (type species)
****** ''[[Methanothrix harundinacea]]'' (Ma ''et al.'' 2006) Akinyemi ''et al.'' 2021
****** ''Methanothrix thermoacetophila'' corrig. Nozhevnikova and Chudina 1988
****** "''Candidatus'' Methanothrix paradoxa" corrig. Angle ''et al.'' 2017
**** Family Methermicoccaceae
***** Genus''Methermicoccus'' Cheng ''et al.'' 2007
****** ''[[Methermicoccus shengliensis]]'' Cheng ''et al.'' 2007 (type species)
* Phylum [[Methanobacteriota]]
** Class [[Methanobacteria]]
*** Order [[Methanobacteriales]]
**** Family [[Methanobacteriaceae]]
***** Genus ''[[Methanobacterium]]'' Kluyver and van Niel 1936
****** ''[[Methanobacterium formicicum]]'' Schnellen 1947 (type species)
****** ''[[Methanobacterium bryantii]]''
***** Genus ''[[Methanobrevibacter]]'' Balch and Wolfe 1981
****** ''[[Methanobrevibacter ruminantium]]'' (Smith and Hungate 1958) Balch and Wolfe 1981 (type species)
****** ''[[Methanobrevibacter acididurans]]'' Savant ''et al.'' 2002
****** ''[[Methanobrevibacter arboriphilicus|Methanobrevibacter arboriphilus]]'' corrig. (Zeikus and Henning 1975) Balch and Wolfe 1981
****** ''[[Methanobrevibacter boviskoreani]]'' Lee ''et al.'' 2013
****** ''[[Methanobrevibacter curvatus]]'' Leadbetter and Breznak 1997
****** ''[[Methanobrevibacter cuticularis]]'' Leadbetter and Breznak 1997
****** ''[[Methanobrevibacter filiformis]]'' Leadbetter ''et al.'' 1998
****** ''[[Methanobrevibacter gottschalkii]]'' Miller and Lin 2002
****** ''[[Methanobrevibacter millerae]]'' Rea ''et al.'' 2007
****** ''[[Methanobrevibacter olleyae]]'' Rea ''et al.'' 2007
****** ''[[Methanobrevibacter oralis]]'' Ferrari ''et al.'' 1995
****** ''[[Methanobrevibacter smithii]]'' Balch and Wolfe 1981
****** ''[[Methanobrevibacter thaueri]]'' Miller and Lin 2002
****** ''[[Methanobrevibacter woesei]]'' Miller and Lin 2002
****** ''[[Methanobrevibacter wolinii]]'' Miller and Lin 2002
****** "''Methanobrevibacter massiliense''" Huynh ''et al.'' 2015
****** "''Candidatus'' Methanobrevibacter intestini" Chibani ''et al.'' 2022
***** Genus ''[[Methanosphaera]]'' Miller and Wolin 1985
****** ''[[Methanosphaera stadtmanae]]'' corrig. Miller and Wolin 1985 (type species)
****** ''[[Methanosphaera cuniculi]]'' Biavati ''et al.'' 1990
***** Genus ''[[Methanothermobacter]]'' Wasserfallen ''et al.'' 2000
****** ''[[Methanothermobacter thermautotrophicus]]'' corrig. (Zeikus and Wolfe 1972) Wasserfallen et al. 2000 (type species)
****** ''Methanothermobacter crinale'' Cheng et al. 2012
****** ''[[Methanothermobacter defluvii]]'' (Kotelnikova et al. 1994) Boone 2002
****** ''[[Methanothermobacter marburgensis]]'' Wasserfallen et al. 2000
****** ''[[Methanothermobacter tenebrarum]]'' Nakamura et al. 2013
****** ''[[Methanothermobacter thermoflexus]]'' (Kotelnikova et al. 1994) Boone 2002
****** ''[[Methanothermobacter thermophilus]]'' (Laurinavichus et al. 1990) Boone 2002
****** ''[[Methanothermobacter wolfeii|Methanothermobacter wolfei]]'' corrig. (Winter et al. 1985) Wasserfallen et al. 2000
**** Family [[Methanothermaceae]]
***** Genus''[[Methanothermus]]'' Stetter 1982
****** ''[[Methanothermus fervidus]]'' Stetter 1982 (type species)
** Class [[Methanopyri]]
*** Order [[Methanopyrales]]
**** Family [[Methanopyraceae]]
***** Genus''[[Methanopyrus]]'' Kurr ''et al.'' 1992
****** ''[[Methanopyrus kandleri]]'' Kurr ''et al.'' 1992 (type species)
** Class [[Methanococci]]
*** Order [[Methanococcales]]
**** Family [[Methanococcaceae]] Balch and Wolfe 1981
***** Genus''[[Methanococcus]]'' Kluyver and van Niel 1936
****** ''[[Methanococcus vannielii]]'' Stadtman and Barker 1951 (type species)
****** ''[[Methanococcus aeolicus]]''
****** ''[[Methanococcus burtonii]]''
****** ''[[Methanococcus chunghsingensis]]''
****** ''[[Methanococcus deltae]]''
****** ''[[Methanococcus jannaschii]]''
****** ''[[Methanococcus maripaludis]]''
***** Genus''[[Methanofervidicoccus]]''
****** ''[[Methanofervidicoccus abyssi]]'' Sakai ''et al.'' 2019 (type species)
***** Genus''[[Methanothermococcus]]''
****** ''[[Methanothermococcus thermolithotrophicus]]'' (Huber ''et al.'' 1984) Whitman 2002 (type species)
**** Family [[Methanocaldococcaceae]]
***** Genus''[[Methanocaldococcus]]''
****** ''[[Methanocaldococcus jannaschii]]'' (Jones ''et al.'' 1984) Whitman 2002 (type species)
***** Genus''[[Methanotorris]]''
****** ''[[Methanotorris igneus]]'' (Burggraf ''et al.'' 1990) Whitman 2002 (type species)
* Phylum [[Thermoplasmatota]]
** Class [[Thermoplasmata]]
*** Order Methanomassiliicoccales
**** Family Methanomassiliicoccaceae
***** Genus''Methanomassiliicoccus'' Dridi ''et al.'' 2012
****** ''[[Methanomassiliicoccus luminyensis]]'' Dridi ''et al.'' 2012 (type species)
**** Family [[Methanomethylophilaceae]]
***** Genus''[[Methanomethylophilus]]'' Borrel ''et al.'' 2024
****** ''[[Methanomethylophilus alvi]]'' Borrel ''et al.'' 2024 (type species)