[1]

Iliev ID, Ananthakrishnan AN, Guo CJ. 2025. Microbiota in inflammatory bowel disease: mechanisms of disease and therapeutic opportunities. Nature Reviews Microbiology 23:509−524

doi: 10.1038/s41579-025-01163-0
[2]

Woese CR, Fox GE. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the United States of America 74:5088−5090

doi: 10.1073/pnas.74.11.5088
[3]

Kandler O, Hippe H. 1977. Lack of peptidoglycan in the cell walls of Methanosarcina barkeri. Archives of Microbiology 113:57−60

doi: 10.1007/BF00428580
[4]

Boone DR, Whitman WB, Rouvière P. 1993. Diversity and taxonomy of methanogens. In Methanogenesis, ed. Ferry JG. Boston, MA: Springer. pp. 35–80 doi: 10.1007/978-1-4615-2391-8_2
[5]

Conrad R. 2020. Importance of hydrogenotrophic, aceticlastic and methylotrophic methanogenesis for methane production in terrestrial, aquatic and other anoxic environments: a mini review. Pedosphere 30:25−39

doi: 10.1016/S1002-0160(18)60052-9
[6]

Chibani CM, Mahnert A, Borrel G, Almeida A, Werner A, et al. 2022. A catalogue of 1,167 genomes from the human gut archaeome. Nature Microbiology 7:48−61

doi: 10.1038/s41564-021-01020-9
[7]

Chen Q, Lyu W, Pan C, Ma L, Sun Y, et al. 2024. Tracking investigation of archaeal composition and methanogenesis function from parental to offspring pigs. Science of The Total Environment 927:172078

doi: 10.1016/j.scitotenv.2024.172078
[8]

Mohammadzadeh R, Mahnert A, Duller S, Moissl-Eichinger C. 2022. Archaeal key-residents within the human microbiome: characteristics, interactions and involvement in health and disease. Current Opinion in Microbiology 67:102146

doi: 10.1016/j.mib.2022.102146
[9]

Meene A, Gierse L, Schwaiger T, Karte C, Schröder C, et al. 2023. Archaeome structure and function of the intestinal tract in healthy and H1N1 infected swine. Frontiers in Microbiology 14:1250140

doi: 10.3389/fmicb.2023.1250140
[10]

Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, et al. 2007. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proceedings of the National Academy of Sciences of the United States of America 104:10643−10648

doi: 10.1073/pnas.0704189104
[11]

Roccarina D, Lauritano EC, Gabrielli M, Franceschi F, Ojetti V, et al. 2010. The role of methane in intestinal diseases. American Journal of Gastroenterology 105:1250−1256

doi: 10.1038/ajg.2009.744
[12]

DiBaise JK, Zhang H, Crowell MD, Krajmalnik-Brown R, Decker GA, et al. 2008. Gut microbiota and its possible relationship with obesity. Mayo Clinic Proceedings 83:460−469

doi: 10.4065/83.4.460
[13]

Hoegenauer C, Hammer HF, Mahnert A, Moissl-Eichinger C. 2022. Methanogenic archaea in the human gastrointestinal tract. Nature Reviews Gastroenterology & Hepatology 19:805−813

doi: 10.1038/s41575-022-00673-z
[14]

Baquero DP, Medvedeva S, Martin-Gallausiaux C, Pende N, Sartori-Rupp A, et al. 2024. Stable coexistence between an archaeal virus and the dominant methanogen of the human gut. Nature Communications 15:7702

doi: 10.1038/s41467-024-51946-x
[15]

Thomas CM, Desmond-Le Quéméner E, Gribaldo S, Borrel G. 2022. Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom. Nature Communications 13:3358

doi: 10.1038/s41467-022-31038-4
[16]

Minnebo Y, De Paepe K, Props R, Lacoere T, Boon N, et al. 2024. Methanogenic archaea quantification in the human gut microbiome with F420 autofluorescence-based flow cytometry. Applied Microbiology 4:162−180

doi: 10.3390/applmicrobiol4010012
[17]

Guindo CO, Drancourt M, Grine G. 2020. Digestive tract methanodrome: physiological roles of human microbiota-associated methanogens. Microbial Pathogenesis 149:104425

doi: 10.1016/j.micpath.2020.104425
[18]

Jones WJ, Nagle DP Jr, Whitman WB. 1987. Methanogens and the diversity of archaebacteria. Microbiological Reviews 51:135−177

doi: 10.1128/mr.51.1.135-177.1987
[19]

Teigen L, Mathai PP, Matson M, Lopez S, Kozysa D, et al. 2021. Methanogen abundance thresholds capable of differentiating in vitro methane production in human stool samples. Digestive Diseases and Sciences 66:3822−3830

doi: 10.1007/s10620-020-06721-5
[20]

Rinke C, Chuvochina M, Mussig AJ, Chaumeil PA, Davín AA, et al. 2021. A standardized archaeal taxonomy for the Genome Taxonomy Database. Nature Microbiology 6:946−959

doi: 10.1038/s41564-021-00918-8
[21]

Iino T, Tamaki H, Tamazawa S, Ueno Y, Ohkuma M, et al. 2013. 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. Microbes and Environments 28:244−250

doi: 10.1264/jsme2.ME12189
[22]

Adam PS, Borrel G, Brochier-Armanet C, Gribaldo S. 2017. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. The ISME Journal 11:2407−2425

doi: 10.1038/ismej.2017.122
[23]

Borrel G, Adam PS, McKay LJ, Chen LX, Sierra-García IN, et al. 2019. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nature Microbiology 4:603−613

doi: 10.1038/s41564-019-0363-3
[24]

Evans PN, Boyd JA, Leu AO, Woodcroft BJ, Parks DH, et al. 2019. An evolving view of methane metabolism in the Archaea. Nature Reviews Microbiology 17:219−32

doi: 10.1038/s41579-018-0136-7
[25]

Sorokin DY, Merkel AY, Abbas B, Makarova KS, Rijpstra WIC, et al. 2018. 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. International Journal of Systematic and Evolutionary Microbiology 68:2199−2208

doi: 10.1099/ijsem.0.002810
[26]

Whitman WB, Bowen TL, Boone DR. 2014. The methanogenic bacteria. In The Prokaryotes, eds Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. Berlin, Heidelberg: Springer. pp. 123–163 doi: 10.1007/978-3-642-38954-2_407
[27]

Lyu Z, Shao N, Akinyemi T, Whitman WB. 2018. Methanogenesis. Current Biology 28:R727−R732

doi: 10.1016/j.cub.2018.05.021
[28]

Fricke WF, Seedorf H, Henne A, Krüer M, Liesegang H, et al. 2006. The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. Journal of Bacteriology 188:642−658

doi: 10.1128/JB.188.2.642-658.2006
[29]

Saengkerdsub S, Ricke SC. 2014. Ecology and characteristics of methanogenic archaea in animals and humans. Critical Reviews in Microbiology 40:97−116

doi: 10.3109/1040841X.2013.763220
[30]

Guindo CO, Davoust B, Drancourt M, Grine G. 2021. Diversity of methanogens in animals' gut. Microorganisms 9:13

doi: 10.3390/microorganisms9010013
[31]

Youngblut ND, Reischer GH, Dauser S, Maisch S, Walzer C, et al. 2021. Vertebrate host phylogeny influences gut archaeal diversity. Nature Microbiology 6:1443−1454

doi: 10.1038/s41564-021-00980-2
[32]

Moissl-Eichinger C, Pausan M, Taffner J, Berg G, Bang C, et al. 2018. Archaea are interactive components of complex microbiomes. Trends in Microbiology 26:70−85

doi: 10.1016/j.tim.2017.07.004
[33]

Chaudhary PP, Conway PL, Schlundt J. 2018. Methanogens in humans: potentially beneficial or harmful for health. Applied Microbiology and Biotechnology 102:3095−3104

doi: 10.1007/s00253-018-8871-2
[34]

Dridi B, Henry M, El Khéchine A, Raoult D, Drancourt M. 2009. High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One 4:e7063

doi: 10.1371/journal.pone.0007063
[35]

Dridi B, Fardeau ML, Ollivier B, Raoult D, Drancourt M. 2012. Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. International Journal of Systematic and Evolutionary Microbiology 62:1902−1907

doi: 10.1099/ijs.0.033712-0
[36]

Borrel G, Harris HMB, Parisot N, Gaci N, Tottey W, et al. 2013. Genome sequence of "Candidatus Methanomassiliicoccus intestinalis" issoire-Mx1, a third thermoplasmatales-related methanogenic archaeon from human feces. Genome Announcements 1:e00453-13

doi: 10.1128/genomea.00453-13
[37]

Biavati B, Vasta M, Ferry JG. 1988. Isolation and characterization of "Methanosphaera cuniculi" sp. nov. Applied and Environmental Microbiology 54:768−771

doi: 10.1128/aem.54.3.768-771.1988
[38]

Borrel G, McCann A, Deane J, Neto MC, Lynch DB, et al. 2017. Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome. The ISME Journal 11:2059−2074

doi: 10.1038/ismej.2017.72
[39]

Luo YH, Su Y, Wright AG, Zhang LL, Smidt H, et al. 2012. Lean breed Landrace pigs harbor fecal methanogens at higher diversity and density than obese breed Erhualian pigs. Archaea 2012:605289

doi: 10.1155/2012/605289
[40]

Mi J, Peng H, Wu Y, Wang Y, Liao X. 2019. Diversity and community of methanogens in the large intestine of finishing pigs. BMC Microbiology 19:83

doi: 10.1186/s12866-019-1459-x
[41]

Misiukiewicz A, Gao M, Filipiak W, Cieslak A, Patra AK, et al. 2021. Review: methanogens and methane production in the digestive systems of nonruminant farm animals. Animal 15:100060

doi: 10.1016/j.animal.2020.100060
[42]

Velasco-Galilea M, Piles M, Viñas M, Rafel O, González-Rodríguez O, et al. 2018. Rabbit microbiota changes throughout the intestinal tract. Frontiers in Microbiology 9:2144

doi: 10.3389/fmicb.2018.02144
[43]

Kušar D, Avguštin G. 2010. Molecular profiling and identification of methanogenic archaeal species from rabbit caecum: new methanogens from rabbit caecum. FEMS Microbiology Ecology 74:623−630

doi: 10.1111/j.1574-6941.2010.00980.x
[44]

Togo AH, Grine G, Khelaifia S, Des Robert C, Brevaut V, et al. 2019. Culture of methanogenic archaea from human colostrum and milk. Scientific Reports 9:18653

doi: 10.1038/s41598-019-54759-x
[45]

Roswall J, Olsson LM, Kovatcheva-Datchary P, Nilsson S, Tremaroli V, et al. 2021. Developmental trajectory of the healthy human gut microbiota during the first 5 years of life. Cell Host & Microbe 29:765−776.e3

doi: 10.1016/j.chom.2021.02.021
[46]

Feehan B, Ran Q, Dorman V, Rumback K, Pogranichniy S, et al. 2023. Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea. Animal Microbiome 5:35

doi: 10.1186/s42523-023-00256-6
[47]

Federici S, Miragoli F, Pisacane V, Rebecchi A, Morelli L, et al. 2015. Archaeal microbiota population in piglet feces shifts in response to weaning: Methanobrevibacter smithii is replaced with Methanobrevibacter boviskoreani. FEMS Microbiology Letters 362:fnv064

doi: 10.1093/femsle/fnv064
[48]

Cao Z, Liang JB, Liao XD, Wright ADG, Wu YB, et al. 2016. Effect of dietary fiber on the methanogen community in the hindgut of Lantang gilts. Animal 10:1666−1676

doi: 10.1017/S1751731116000525
[49]

Kamke J, Kittelmann S, Soni P, Li Y, Tavendale M, et al. 2016. Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation. Microbiome 4:56

doi: 10.1186/s40168-016-0201-2
[50]

Lee GI, Hedemann MS, Jørgensen H, Bach Knudsen KE. 2022. Influence of dietary fibre on nutrient digestibility and energy utilisation in growing pigs fed diets varying in soluble and insoluble fibres from co-products. Animal 16:100511

doi: 10.1016/j.animal.2022.100511
[51]

Li H, Qu J, Li T, Yao M, Li J, et al. 2017. Gut microbiota may predict host divergence time during Glires evolution. FEMS Microbiology Ecology 93:fix009

doi: 10.1093/femsec/fix009
[52]

Seradj AR, Balcells J, Morazan H, Alvarez-Rodriguez J, Babot D, et al. 2018. The impact of reducing dietary crude protein and increasing total dietary fiber on hindgut fermentation, the methanogen community and gas emission in growing pigs. Animal Feed Science and Technology 245:54−66

doi: 10.1016/j.anifeedsci.2018.09.005
[53]

Cisek AA, Szymańska E, Wierzbicka-Rucińska A, Aleksandrzak-Piekarczyk T, Cukrowska B. 2024. Methanogenic Archaea in the pediatric inflammatory bowel disease in relation to disease type and activity. International Journal of Molecular Sciences 25:673

doi: 10.3390/ijms25010673
[54]

Scanlan PD, Shanahan F, Marchesi JR. 2008. Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiology 8:79

doi: 10.1186/1471-2180-8-79
[55]

Khelaifia S, Drancourt M. 2012. Susceptibility of archaea to antimicrobial agents: applications to clinical microbiology. Clinical Microbiology and Infection 18:841−848

doi: 10.1111/j.1469-0691.2012.03913.x
[56]

Ueno Y, Yamada K, Yoshida N, Maruyama S, Isozaki Y. 2006. Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era. Nature 440:516−519

doi: 10.1038/nature04584
[57]

Kumpitsch C, Fischmeister FPS, Mahnert A, Lackner S, Wilding M, et al. 2021. Reduced B12 uptake and increased gastrointestinal formate are associated with archaeome-mediated breath methane emission in humans. Microbiome 9:193

doi: 10.1186/s40168-021-01130-w
[58]

Liu Y, Whitman WB. 2008. Metabolic, phylogenetic, and ecological diversity of the methanogenic Archaea. Annals of the New York Academy of Sciences 1125:171−189

doi: 10.1196/annals.1419.019
[59]

Ferrari A, Brusa T, Rutili A, Canzi E, Biavati B. 1994. Isolation and characterization of Methanobrevibacter oralis sp. nov. Current Microbiology 29:7−12

doi: 10.1007/BF01570184
[60]

Khelaifia S, Garibal M, Robert C, Raoult D, Drancourt M. 2014. Draft genome sequence of a human-associated isolate of Methanobrevibacter arboriphilicus, the lowest-G+C-content archaeon. Genome Announcements 2:e01181-13

doi: 10.1128/genomea.01181-13
[61]

Miller TL, Wolin MJ, Kusel EA. 1986. Isolation and characterization of methanogens from animal feces. Systematic and Applied Microbiology 8:234−238

doi: 10.1016/S0723-2020(86)80084-4
[62]

Sengupta A, Ghosh I, Mallick J, Thakur AR, Datta K. 2004. Presence of a human hyaluronan binding protein 1 (HABP1) pseudogene-like sequence in Methanosarcina barkeri suggests its linkage in evolution. DNA and Cell Biology 23:301−310

doi: 10.1089/104454904323090930
[63]

Borrel G, Harris HMB, Tottey W, Mihajlovski A, Parisot N, et al. 2012. Genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens. Journal of Bacteriology 194:6944−6945

doi: 10.1128/JB.01867-12
[64]

Kröninger L, Steiniger F, Berger S, Kraus S, Welte CU, et al. 2019. Energy conservation in the gut microbe Methanomassiliicoccus luminyensis is based on membrane-bound ferredoxin oxidation coupled to heterodisulfide reduction. The FEBS Journal 286:3831−3843

doi: 10.1111/febs.14948
[65]

Ellermann J, Hedderich R, Böcher R, Thauer RK. 1988. The final step in methane formation. Investigations with highly purified methyl-CoM reductase (component C) from Methanobacterium thermoautotrophicum (strain Marburg). European Journal of Biochemistry 172:669−677

doi: 10.1111/j.1432-1033.1988.tb13941.x
[66]

Hallam SJ, Girguis PR, Preston CM, Richardson PM, DeLong EF. 2003. Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing Archaea. Applied and Environmental Microbiology 69:5483−5491

doi: 10.1128/AEM.69.9.5483-5491.2003
[67]

Ermler U, Grabarse W, Shima S, Goubeaud M, Thauer RK. 1997. Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Science 278:1457−1462

doi: 10.1126/science.278.5342.1457
[68]

Goubeaud M, Schreiner G, Thauer RK. 1997. Purified methyl-coenzyme-M reductase is activated when the enzyme-bound coenzyme F430 is reduced to the nickel(I) oxidation state by titanium(III) citrate. European Journal of Biochemistry 243:110−114

doi: 10.1111/j.1432-1033.1997.00110.x
[69]

Prakash D, Wu Y, Suh SJ, Duin EC. 2014. Elucidating the process of activation of methyl-coenzyme M reductase. Journal of Bacteriology 196:2491−2498

doi: 10.1128/JB.01658-14
[70]

Duin EC, Wagner T, Shima S, Prakash D, Cronin B, et al. 2016. Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol. Proceedings of the National Academy of Sciences of the United States of America 113:6172−6177

doi: 10.1073/pnas.1600298113
[71]

Hinderberger D, Piskorski RP, Goenrich M, Thauer RK, Schweiger A, et al. 2006. A nickel–alkyl bond in an inactivated state of the enzyme catalyzing methane formation. Angewandte Chemie International Edition 45:3602−3607

doi: 10.1002/anie.200600366
[72]

Hedderich R, Thauer RK. 1988. Methanobacterium thermoautotrophicum contains a soluble enzyme system that specifically catalyzes the reduction of the heterodisulfide of coenzyme M and 7-mercaptoheptanoylthreonine phosphate with H2. FEBS Letters 234:223−227

doi: 10.1016/0014-5793(88)81339-5
[73]

Stojanowic A, Mander GJ, Duin EC, Hedderich R. 2003. Physiological role of the F420-non-reducing hydrogenase (Mvh) from Methanothermobacter marburgensis. Archives of Microbiology 180:194−203

doi: 10.1007/s00203-003-0577-9
[74]

Hamann N, Mander GJ, Shokes JE, Scott RA, Bennati M, et al. 2007. A cysteine-rich CCG domain contains a novel [4Fe-4S] cluster binding motif as deduced from studies with subunit B of heterodisulfide reductase from Methanothermobacter marburgensis. Biochemistry 46:12875−122885

doi: 10.1021/bi700679u
[75]

Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R. 2008. Methanogenic archaea: ecologically relevant differences in energy conservation. Nature Reviews Microbiology 6:579−591

doi: 10.1038/nrmicro1931
[76]

Wagner T, Koch J, Ermler U, Shima S. 2017. Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction. Science 357:699−703

doi: 10.1126/science.aan0425
[77]

Buckel W, Thauer RK. 2018. Flavin-based electron bifurcation, a new mechanism of biological energy coupling. Chemical Reviews 118:3862−3886

doi: 10.1021/acs.chemrev.7b00707
[78]

Kaster A-K, Moll J, Parey K, Thauer RK. 2011. Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. Proceedings of the National Academy of Sciences of the United States of America 108:2981−2986

doi: 10.1073/pnas.1016761108
[79]

Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson FL. 2013. The prokaryotes: prokaryotic physiology and biochemistry. Berlin, Heidelberg: Springer. 461 pp doi: 10.1007/978-3-642-30141-4
[80]

Berg IA. 2011. Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Applied and Environmental Microbiology 77:1925−1936

doi: 10.1128/AEM.02473-10
[81]

Berghuis BA, Yu FB, Schulz F, Blainey PC, Woyke T, et al. 2019. Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. Proceedings of the National Academy of Sciences of the United States of America 116:5037−5044

doi: 10.1073/pnas.1815631116
[82]

Abdul Halim MF, Day LA, Costa KC. 2021. Formate-dependent heterodisulfide reduction in a Methanomicrobiales archaeon. Applied and Environmental Microbiology 87:e02698-20

doi: 10.1128/aem.02698-20
[83]

Wagner T, Ermler U, Shima S. 2016. The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters. Science 354:114−117

doi: 10.1126/science.aaf9284
[84]

Acharya P, Warkentin E, Ermler U, Thauer RK, Shima S. 2006. The structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes. Journal of Molecular Biology 357:870−879

doi: 10.1016/j.jmb.2006.01.015
[85]

Ceh K, Demmer U, Warkentin E, Moll J, Thauer RK, et al. 2009. Structural basis of the hydride transfer mechanism in F420-dependent methylenetetrahydromethanopterin dehydrogenase. Biochemistry 48:10098−10105

doi: 10.1021/bi901104d
[86]

Zirngibl C, Hedderich R, Thauer RK. 1990. N5,N10-Methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum has hydrogenase activity. FEBS Letters 261:112−116

doi: 10.1016/0014-5793(90)80649-4
[87]

Welander PV, Metcalf WW. 2005. Loss of the mtr operon in Methanosarcina blocks growth on methanol, but not methanogenesis, and reveals an unknown methanogenic pathway. Proceedings of the National Academy of Sciences of the United States of America 102:10664−10669

doi: 10.1073/pnas.0502623102
[88]

Ferry JG. 2020. Methanosarcina acetivorans: a model for mechanistic understanding of aceticlastic and reverse methanogenesis. Frontiers in Microbiology 11:1806

doi: 10.3389/fmicb.2020.01806
[89]

Zhou J, Smith JA, Li M, Holmes DE, Hazen TC. 2023. Methane production by Methanothrix thermoacetophila via direct interspecies electron transfer with Geobacter metallireducens. mBio 14:e00360-23

doi: 10.1128/mbio.00360-23
[90]

Holmes DE, Shrestha PM, Walker DJF, Dang Y, Nevin KP, et al. 2017. Metatranscriptomic evidence for direct interspecies electron transfer between geobacter and methanothrix species in methanogenic rice paddy soils. Applied and Environmental Microbiology 83:e00223-17

doi: 10.1128/aem.00223-17
[91]

Rother M, Metcalf WW. 2004. Anaerobic growth of Methanosarcina acetivorans C2A on carbon monoxide: an unusual way of life for a methanogenic archaeon. Proceedings of the National Academy of Sciences of the United States of America 101:16929−16934

doi: 10.1073/pnas.0407486101
[92]

Jetten MSM, Stams AJM, Zehnder AJB. 1992. Methanogenesis from acetate: a comparison of the acetate metabolism in Methanothrix soehngenii and Methanosarcina spp. FEMS Microbiology Reviews 8:181−197

doi: 10.1016/0378-1097(92)90802-u
[93]

Möller-Zinkhan D, Thauer RK. 1990. Anaerobic lactate oxidation to 3 CO2 by Archaeoglobus fulgidus via the carbon monoxide dehydrogenase pathway: demonstration of the acetyl-CoA carbon-carbon cleavage reaction in cell extracts. Archives of Microbiology 153:215−218

doi: 10.1007/BF00249070
[94]

Borrel G, O'Toole PW, Harris HMB, Peyret P, Brugère JF, et al. 2013. Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis. Genome Biology and Evolution 5:1769−1780

doi: 10.1093/gbe/evt128
[95]

Welte C, Deppenmeier U. 2014. Bioenergetics and anaerobic respiratory chains of aceticlastic methanogens. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1837:1130−1147

doi: 10.1016/j.bbabio.2013.12.002
[96]

Bose A, Pritchett MA, Metcalf WW. 2008. Genetic analysis of the methanol- and methylamine-specific methyltransferase 2 genes of Methanosarcina acetivorans C2A. Journal of Bacteriology 190:4017−4026

doi: 10.1128/JB.00117-08
[97]

Ferguson DJ, Gorlatova N, Grahame DA, Krzycki JA. 2000. Reconstitution of dimethylamine: coenzyme M methyl transfer with a discrete corrinoid protein and two methyltransferases purified from Methanosarcina barkeri. Journal of Biological Chemistry 275:29053−29060

doi: 10.1074/jbc.M910218199
[98]

Van Der Meijden P, Heythuysen HJ, Pouwels A, Houwen F, Van Der Drift C, et al. 1983. Methyltransferases involved in methanol conversion by Methanosarcina barkeri. Archives of Microbiology 134:238−242

doi: 10.1007/BF00407765
[99]

Zhang CJ, Pan J, Liu Y, Duan CH, Li M. 2020. Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments. Microbiome 8:94

doi: 10.1186/s40168-020-00876-z
[100]

De La Cuesta-Zuluaga J, Spector TD, Youngblut ND, Ley RE. 2021. Genomic insights into adaptations of trimethylamine-utilizing methanogens to diverse habitats, including the human gut. mSystems 6:e00939-20

doi: 10.1128/msystems.00939-20
[101]

Miller TL, Wolin MJ. 1985. Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen. Archives of Microbiology 141:116−122

doi: 10.1007/BF00423270
[102]

Peng Y, Xie T, Wu Z, Zheng W, Zhang T, et al. 2022. Archaea: an under-estimated kingdom in livestock animals. Frontiers in Veterinary Science 9:973508

doi: 10.3389/fvets.2022.973508
[103]

Yao H, Flanagan BM, Williams BA, Mikkelsen D, Gidley MJ. 2023. Lactate and buyrate proportions, methanogen growth and gas production during in vitro dietary fibre fermentation all depend on fibre concentration. Food Hydrocolloids 134:108061

doi: 10.1016/j.foodhyd.2022.108061
[104]

Wang Z, Wang S, Hu Y, Du B, Meng J, et al. 2022. Distinguishing responses of acetoclastic and hydrogenotrophic methanogens to ammonia stress in mesophilic mixed cultures. Water Research 224:119029

doi: 10.1016/j.watres.2022.119029
[105]

Deng F, Peng Y, Zhang Z, Howe S, Wu Z, et al. 2022. Weaning time affects the archaeal community structure and functional potential in pigs. Frontiers in Microbiology 13:845621

doi: 10.3389/fmicb.2022.845621
[106]

Deng F, Li Y, Peng Y, Wei X, Wang X, et al. 2021. The diversity, composition, and metabolic pathways of archaea in pigs. Animals 11:2139

doi: 10.3390/ani11072139
[107]

Kurade MB, Saha S, Salama ES, Patil SM, Govindwar SP, et al. 2019. Acetoclastic methanogenesis led by Methanosarcina in anaerobic co-digestion of fats, oil and grease for enhanced production of methane. Bioresource Technology 272:351−359

doi: 10.1016/j.biortech.2018.10.047
[108]

Cao Z, Liao X, Liang J, Wu Y, Yu B. 2014. Diversity of methanogens in the hindgut of grower and finisher pigs. African Journal of Biotechnology 11(21):4949−4955

doi: 10.4314/ajb.v11i21
[109]

Mafra D, Ribeiro M, Fonseca L, Regis B, Cardozo LFMF, et al. 2022. Archaea from the gut microbiota of humans: could be linked to chronic diseases? Anaerobe 77:102629

doi: 10.1016/j.anaerobe.2022.102629
[110]

Cisek AA, Szymańska E, Aleksandrzak-Piekarczyk T, Cukrowska B. 2024. The role of methanogenic archaea in inflammatory bowel disease—a review. Journal of Personalized Medicine 14:196

doi: 10.3390/jpm14020196
[111]

Lyu Z. 2021. Back to the source: molecular identification of methanogenic archaea as markers of colonic methane production. Digestive Diseases and Sciences 66:3661−3664

doi: 10.1007/s10620-021-06839-0
[112]

Talamantes S, Steiner F, Spencer S, Neshatian L, Sonu I. 2024. Intestinal methanogen overgrowth (IMO) is associated with delayed small bowel and colonic transit time (TT) on the wireless motility capsule (WMC). Digestive Diseases and Sciences 69:3361−3368

doi: 10.1007/s10620-024-08563-x
[113]

Stothart MR, McLoughlin PD, Medill SA, Greuel RJ, Wilson AJ, et al. 2024. Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses. Nature Communications 15:6012

doi: 10.1038/s41467-024-49963-x
[114]

Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, et al. 2014. Human genetics shape the gut microbiome. Cell 159:789−799

doi: 10.1016/j.cell.2014.09.053
[115]

Attaluri A, Jackson M, Valestin J, Rao SS. 2010. Methanogenic flora is associated with altered colonic transit but not stool characteristics in constipation without IBS. American Journal of Gastroenterology 105:1407−1411

doi: 10.1038/ajg.2009.655
[116]

Villanueva-Millan MJ, Leite G, Wang J, Morales W, Parodi G, et al. 2022. Methanogens and hydrogen sulfide producing bacteria guide distinct gut microbe profiles and irritable bowel syndrome subtypes. The American Journal of Gastroenterology 117:2055−2066

doi: 10.14309/ajg.0000000000001997
[117]

Villanueva-Millan MJ, Leite G, Morales W, Sanchez M, Parodi G, et al. 2024. Hydrogen sulfide producers drive a diarrhea-like phenotype and a methane producer drives a constipation-like phenotype in animal models. Digestive Diseases and Sciences 69:426−436

doi: 10.1007/s10620-023-08197-5
[118]

Blais Lecours P, Marsolais D, Cormier Y, Berberi M, Haché C, et al. 2014. Increased prevalence of Methanosphaera stadtmanae in inflammatory bowel diseases. PLoS One 9:e87734

doi: 10.1371/journal.pone.0087734
[119]

Vierbuchen T, Bang C, Rosigkeit H, Schmitz RA, Heine H. 2017. The human-associated archaeon Methanosphaera stadtmanae is recognized through its RNA and induces TLR8-dependent NLRP3 inflammasome activation. Frontiers in Immunology 8:1535

doi: 10.3389/fimmu.2017.01535
[120]

Bang C, Weidenbach K, Gutsmann T, Heine H, Schmitz RA. 2014. The intestinal archaea Methanosphaera stadtmanae and Methanobrevibacter smithii activate human dendritic cells. PLoS One 9:e99411

doi: 10.1371/journal.pone.0099411
[121]

Coker OO, Wu WKK, Wong SH, Sung JJY, Yu J. 2020. Altered gut archaea composition and interaction with bacteria are associated with colorectal cancer. Gastroenterology 159:1459−1470.e5

doi: 10.1053/j.gastro.2020.06.042
[122]

Zhou X, Liu Y, Xiong X, Chen J, Tang W, et al. 2022. Intestinal accumulation of microbiota-produced succinate caused by loss of microRNAs leads to diarrhea in weanling piglets. Gut Microbes 14:2091369

doi: 10.1080/19490976.2022.2091369
[123]

Armougom F, Henry M, Vialettes B, Raccah D, Raoult D. 2009. Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and methanogens in anorexic patients. PLoS One 4:e7125

doi: 10.1371/journal.pone.0007125
[124]

Borrel G, Gaci N, Peyret P, O'Toole PW, Gribaldo S, et al. 2014. Unique characteristics of the pyrrolysine system in the 7th order of methanogens: implications for the evolution of a genetic code expansion cassette. Archaea 2014:374146

doi: 10.1155/2014/374146
[125]

Tang WHW, Wang Z, Kennedy DJ, Wu Y, Buffa JA, et al. 2015. Gut microbiota-dependent trimethylamine N-oxide (TMAO) pathway contributes to both development of renal insufficiency and mortality risk in chronic kidney disease. Circulation Research 116:448−455

doi: 10.1161/CIRCRESAHA.116.305360
[126]

Brugère JF, Borrel G, Gaci N, Tottey W, O'Toole PW, et al. 2014. Archaebiotics: proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease. Gut Microbes 5:5−10

doi: 10.4161/gmic.26749
[127]

Woh PY, Chen Y, Kumpitsch C, Mohammadzadeh R, Schmidt L, et al. 2025. Reevaluation of the gastrointestinal methanogenic archaeome in multiple sclerosis and its association with treatment. Microbiology Spectrum 13:e02183-24

doi: 10.1128/spectrum.02183-24
[128]

Krishnan L, Deschatelets L, Stark FC, Gurnani K, Sprott GD. 2010. Archaeosome adjuvant overcomes tolerance to tumor-associated melanoma antigens inducing protective CD8+ T cell responses. Journal of Immunology Research 2010:578432

doi: 10.1155/2010/578432
[129]

Stark FC, Akache B, Ponce A, Dudani R, Deschatelets L, et al. 2019. Archaeal glycolipid adjuvanted vaccines induce strong influenza-specific immune responses through direct immunization in young and aged mice or through passive maternal immunization. Vaccine 37:7108−7116

doi: 10.1016/j.vaccine.2019.07.010
[130]

Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, et al. 2016. Alterations of the human gut microbiome in multiple sclerosis. Nature Communications 7:12015

doi: 10.1038/ncomms12015
[131]

Bang C, Vierbuchen T, Gutsmann T, Heine H, Schmitz RA. 2017. Immunogenic properties of the human gut-associated archaeon Methanomassiliicoccus luminyensis and its susceptibility to antimicrobial peptides. PLoS One 12:e0185919

doi: 10.1371/journal.pone.0185919
[132]

Bang C, Schilhabel A, Weidenbach K, Kopp A, Goldmann T, et al. 2012. Effects of antimicrobial peptides on methanogenic archaea. Antimicrobial Agents and Chemotherapy 56:4123−4130

doi: 10.1128/AAC.00661-12
[133]

Nkamga VD, Henrissat B, Drancourt M. 2017. Archaea: essential inhabitants of the human digestive microbiota. Human Microbiome Journal 3:1−8

doi: 10.1016/j.humic.2016.11.005
[134]

Ruaud A, Esquivel-Elizondo S, De La Cuesta-Zuluaga J, Waters JL, Angenent LT, et al. 2020. Syntrophy via interspecies H2 transfer between Christensenella and Methanobrevibacter underlies their global cooccurrence in the human gut. mBio 11:e03235-19

doi: 10.1128/mbio.03235-19
[135]

Rey FE, Gonzalez MD, Cheng J, Wu M, Ahern PP, et al. 2013. Metabolic niche of a prominent sulfate-reducing human gut bacterium. Proceedings of the National Academy of Sciences of the United States of America 110:13582−13587

doi: 10.1073/pnas.1312524110
[136]

Feldewert C, Lang K, Brune A. 2020. The hydrogen threshold of obligately methyl-reducing methanogens. FEMS Microbiology Letters 367:fnaa137

doi: 10.1093/femsle/fnaa137
[137]

Wang T, Van Dijk L, Rijnaarts I, Hermes GDA, De Roos NM, et al. 2022. Methanogen levels are significantly associated with fecal microbiota composition and alpha diversity in healthy adults and irritable bowel syndrome patients. Microbiology Spectrum 10:e01653-22

doi: 10.1128/spectrum.01653-22
[138]

Traore SI, Khelaifia S, Armstrong N, Lagier JC, Raoult D. 2019. Isolation and culture of Methanobrevibacter smithii by co-culture with hydrogen-producing bacteria on agar plates. Clinical Microbiology and Infection 25:1561.e1−1561.e5

doi: 10.1016/j.cmi.2019.04.008
[139]

Smith NW, Shorten PR, Altermann E, Roy NC, McNabb WC. 2020. Competition for hydrogen prevents coexistence of human gastrointestinal hydrogenotrophs in continuous culture. Frontiers in Microbiology 11:1073

doi: 10.3389/fmicb.2020.01073
[140]

Park T, Cheong H, Yoon J, Kim A, Yun Y, et al. 2021. Comparison of the fecal microbiota of horses with intestinal disease and their healthy counterparts. Veterinary Sciences 8:113

doi: 10.3390/vetsci8060113