Hackstein JH, Stumm CK. Methane production in terrestrial arthropods. Proc Natl Acad Sci USA. 1994;91:5441–5.
Hackstein JHP, van Alen TA. Fecal methanogens and vertebrate evolution. Evolution. 1996;50:559–72.
Borrel G, McCann A, Deane J, Neto MC, Lynch DB, Brugère JF, et al. Genomics and metagenomics of trimethylamine-utilizing archaea in the human gut microbiome. ISME J. 2017;11:2059–74.
Raymann K, Moeller AH, Goodman AL, Ochman H. Unexplored archaeal diversity in the great ape gut microbiome. mSphere. 2017;2:e00026-17.
Douglas AE. Multiorganismal insects: diversity and function of resident microorganisms. Annu Rev Entomol. 2015;60:17–34.
Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, Fulton R, et al. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci USA. 2007;104:10643–8.
Gaci N, Borrel G, Tottey W, O’Toole PW, Brugère JF. Archaea and the human gut: new beginning of an old story. World J Gastroenterol. 2014;20:16062–78.
Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, et al. The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS ONE. 2010;5:e8926.
Lang K, Schuldes J, Klingl A, Poehlein A, Daniel R, Brunea A. New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of ‘Candidatus Methanoplasma termitum’. Appl Environ Microbiol. 2015;81:1338–52.
Borrel G, Brugère JF, Gribaldo S, Schmitz RA, Moissl-Eichinger C. The host-associated archaeome. Nat Rev Microbiol. 2020;18:622–36.
Sprenger WW, van Belzen MC, Rosenberg J, Hackstein JH, Keltjens JT. Methanomicrococcus blatticola gen. nov., sp. nov., a methanol- and methylamine-reducing methanogen from the hindgut of the cockroach Periplaneta americana. Int J Syst Evol Microbiol. 2000;50:1989–99.
Jarvis GN, Strömpl C, Burgess DM, Skillman LC, Moore ER, Joblin KN. Isolation and identification of ruminal methanogens from grazing cattle. Curr Microbiol. 2000;40:327–32.
Lambie SC, Kelly WJ, Leahy SC, Li D, Reilly K, McAllister TA, et al. The complete genome sequence of the rumen methanogen Methanosarcina barkeri CM1. Stand Genomic Sci. 2015;10:57.
Brune, A. Methanogens in the digestive tract of termites. In: Hackstein JHP, editor. (Endo)symbiotic methanogenic archaea. Berlin: Springer; 2018. p. 81–101.
Li Z, Wang X, Alberdi A, Deng J, Zhong Z, Si H, et al. Comparative microbiome analysis reveals the ecological relationships between rumen methanogens, acetogens, and their hosts. Front Microbiol. 2020;11:1311.
Sprenger WW, Hackstein JHP, Keltjens JT. The energy metabolism of Methanomicrococcus blatticola: physiological and biochemical aspects. Antonie van Leeuwenhoek. 2005;87:289–99.
Sprenger WW, Hackstein JHP, Keltjens JT. The competitive success of Methanomicrococcus blatticola, a dominant methylotrophic methanogen in the cockroach hindgut, is supported by high substrate affinities and favorable thermodynamics. FEMS Microbiol Ecol. 2007;60:266–75.
Borrel G, Adam PS, McKay LJ, Chen LX, Sierra-García IN, Sieber C, et al. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nat Microbiol. 2019;4:603–13.
Nobu MK, Narihiro T, Kuroda K, Mei R, Liu WT. Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen. ISME J. 2016;10:2478–87.
Sorokin DY, Makarova KS, Abbas B, Ferrer M, Golyshin PN, Galinski EA, et al. Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis. Nat Microbiol. 2017;2:17081.
Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ, Hugenholtz P, et al. Methylotrophic methanogenesis discovered in the novel archaeal phylum Verstraetearchaeota. Nat Microbiol. 2016;1:16170.
Borrel G, O’Toole PW, Harris HM, Peyret P, Brugère JF, Gribaldo S. Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis. Genome Biol Evol. 2013;5:1769–80.
Söllinger A, Urich T. Methylotrophic methanogens everywhere—physiology and ecology of novel players in global methane cycling. Biochem Soc Trans. 2019;47:1895–907.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.
Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol. 2016;428:726–31.
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, et al. EggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019;47:D309–14.
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019;47:D427–32.
Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res. 2003;31:371–3.
Krogh A, Larsson B, Von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305:567–80.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, et al. DbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2018;46:W95–101.
Coutinho PM, Deleury E, Davies GJ, Henrissat B. An evolving hierarchical family classification for glycosyltransferases. J Mol Biol. 2003;328:307–17.
Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2014;2:e243.
Johnson LS, Eddy SR, Portugaly E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics. 2010;11:431.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.
Criscuolo A, Gribaldo S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol. 2010;10:210.
Lartillot N, Lepage T, Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics. 2009;25:2286–8.
Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74.
Miele V, Penel S, Duret L. Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics. 2011;12:116.
Csurös, M. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics. 2010;26:1910–2.
Oren, A. The family methanosarcinaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The Prokaryotes: other major lineages of bacteria and the archaea. Berlin: Springer; 2014. p. 259–81.
Ebbes M, Bleymüller WM, Cernescu M, Nölker R, Brutschy B, Niemann HH. Fold and function of the InlB B-repeat. J Biol Chem. 2011;286:15496–506.
Haft DH, Payne SH, Selengut JD. Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. J Bacteriol. 2012;194:36–48.
Porter NT, Martens EC. The critical roles of polysaccharides in gut microbial ecology and physiology. Annu Rev Microbiol. 2017;71:349–69.
Albers SV, Meyer BH. The archaeal cell envelope. Nat Rev Microbiol. 2011;9:414–26.
Ashhurst DE, Costin NM. Insect mucosubstances. III. Some mucosubstances of the nervous systems of the wax-moth (Galleria mellonella) and the stick insect (Carausius morosus). Histochem J. 1971;3:379–87.
Morita, RY. Bacteria in oligotrophic environments. New York, NY: Chapman & Hall; 1997.
Paula FS, Chin JP, Schnürer A, Müller B, Manesiotis P, Waters N, et al. The potential for polyphosphate metabolism in archaea and anaerobic polyphosphate formation in Methanosarcina mazei. Sci Rep. 2019;9:17101.
Harris RM, Webb DC, Howitt SM, Cox GB. Characterization of PitA and PitB from Escherichia coli. J Bacteriol. 2001;183:5008–14.
Poehlein A, Schneider D, Soh M, Daniel R, Seedorf H. Comparative genomic analysis of members of the genera methanosphaera and methanobrevibacter reveals distinct clades with specific potential metabolic functions. Archaea. 2018;2018:609847.
Borrel G, Parisot N, Harris HM, Peyretaillade E, Gaci N, Tottey W, et al. Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics. 2014;15:679.
Hwang S, Choe D, Yoo M, Cho S, Kim SC, Cho S, et al. Peptide transporter CstA imports pyruvate in Escherichia coli K-12. J Bacteriol. 2018;200:e00771-17.
Rasmussen JJ, Vegge CS, Frøkiær H, Howlett RM, Krogfelt KA, Kelly DJ, et al. Campylobacter jejuni carbon starvation protein A (CstA) is involved in peptide utilization, motility and agglutination, and has a role in stimulation of dendritic cells. J Med Microbiol. 2013;62:1135–43.
Li Y, Leahy SC, Jeyanathan J, Henderson G, Cox F, Altermann E, et al. The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the Methanomassiliicoccales. Stand Genomic Sci. 2016;11:59.
Kelly WJ, Li D, Lambie SC, Jeyanathan J, Cox F, Li Y, et al. Complete genome sequence of methanogenic Archaeon ISO4-G1, a member of the Methanomassiliicoccales, isolated from a sheep rumen. Genome Announc. 2016;4:e00221-16.
Maitra PK, Bhosale SB, Kshirsagar DC, Yeole TY, Shanbhag AN. Metabolite and enzyme profiles of glycogen metabolism in Methanococcoides methylutens. FEMS Microbiol Lett. 2001;198:23–9.
Santiago-Martínez MG, Encalada R, Lira-Silva E, Pineda E, Gallardo-Pérez JC, Reyes-García MA, et al. The nutritional status of Methanosarcina acetivorans regulates glycogen metabolism and gluconeogenesis and glycolysis fluxes. FEBS J. 2016;283:1979–99.
Dobrijevic D, Abraham AL, Jamet A, Maguin E, van de Guchte M. Functional comparison of bacteria from the human gut and closely related non-gut bacteria reveals the importance of conjugation and a paucity of motility and chemotaxis functions in the gut environment. PLoS ONE. 2016;11:e0159030.
Merhej V, Royer-Carenzi M, Pontarotti P, Raoult D. Massive comparative genomic analysis reveals convergent evolution of specialized bacteria. Biol Direct. 2009;4:13.
Fricke WF, Seedorf H, Henne A, Krüer M, Liesegang H, Hedderich R, et al. The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. J Bacteriol. 2006;188:642–58.
Adam PS, Borrel G, Gribaldo S. An archaeal origin of the Wood–Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy. Nat Microbiol. 2019;4:2155–63.
Schröder I, Thauer RK. Methylcobalamin:homocysteine methyltransferase from Methanobacterium thermoautotrophicum. Identification as the metE gene product. Eur J Biochem. 1999;263:789–96.
Krone UE, McFarlan SC, Hogenkamp HPC. Purification and partial characterization of a putative thymidylate synthase from Methanobacterium thermoautotrophicum. Eur J Biochem. 1994;220:789–94.
Muller V, Blaut M, Gottschalk G. Utilization of methanol plus hydrogen by Methanosarcina barkeri for methanogenesis and growth. Appl Environ Microbiol. 1986;52:269–74.
Kato N, Yurimoto H, Thauer RK. The physiological role of the ribulose monophosphate pathway in bacteria and archaea. Biosci Biotechnol Biochem. 2006;70:10–21.
Welte C, Deppenmeier U. Bioenergetics and anaerobic respiratory chains of aceticlastic methanogens. Biochim Biophys Acta Bioenerg. 2014;1837:1130–47.
Kurth JM, den Camp HJMO, Welte CU. Several ways one goal—methanogenesis from unconventional substrates. Appl Microbiol Biotechnol. 2020;104:6839–54.
Meuer J, Kuettner HC, Zhang JK, Hedderich R, Metcalf WW. Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation. Proc Natl Acad Sci USA. 2002;99:5632–7.
Wagner T, Koch J, Ermler U, Shima S. Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction. Science. 2017;357:689–703.
Arshad A, Speth DR, de Graaf RM, Op den Camp HJ, Jetten MS, Welte CU. A metagenomics-based metabolic model of nitrate-dependent anaerobic oxidation of methane by Methanoperedens-like archaea. Front Microbiol. 2015;6:6.
Hedderich R, Whitman WB. Physiology and biochemistry of the methane-producing archaea. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The Prokaryotes – prokaryotic biology and symbiotic associations. Berlin: Springer; 2013. p. 1050–79.
Morgavi DP, Martin C, Jouany JP, Ranilla MJ. Rumen protozoa and methanogenesis: not a simple cause-effect relationship. Br J Nutr. 2012;107:388–97.
Maier RJ, Olczak A, Maier S, Soni S, Gunn J. Respiratory hydrogen use by Salmonella enterica serovar Typhimurium is essential for virulence. Infect Immun. 2004;72:6294–9.
Carbonero F, Benefiel AC, Gaskins HR. Contributions of the microbial hydrogen economy to colonic homeostasis. Nat Rev Gastroenterol Hepatol. 2012;9:504–18.
Kalantar-Zadeh K, Berean KJ, Ha N, Chrimes AF, Xu K, Grando D, et al. A human pilot trial of ingestible electronic capsules capable of sensing different gases in the gut. Nat Electron. 2018;1:79–87.
Conrad R, Phelps TJ, Zeikus JG. Gas metabolism evidence in support of the juxtaposition of hydrogen-producing and methanogenic bacteria in sewage sludge and lake sediments. Appl Environ Microbiol. 1985;50:595–601.
Lovley DR, Goodwin S. Hydrogen concentrations as an indicator of the predominant terminal electron-accepting reactions in aquatic sediments. Geochim Cosmochim Acta. 1988;52:2993–3003.
Hackstein JHP. Genetic and evolutionary constraints for the symbiosis between animals and methanogenic bacteria. Environ Monit Assess. 1996;42:39–56.
Ametaj BN, Zebeli Q, Saleem F, Psychogios N, Lewis MJ, Dunn SM, et al. Metabolomics reveals unhealthy alterations in rumen metabolism with increased proportion of cereal grain in the diet of dairy cows. Metabolomics. 2010;6:583–94.
Mausz MA, Chen Y. Microbiology and ecology of methylated amine metabolism in marine ecosystems. Curr Issues Mol Biol. 2019;33:133–48.
King GM, Klug MJ, Lovley DR. Metabolism of acetate, methanol, and methylated amines in intertidal sediments of Lowes Cove, Maine. Appl Environ Microbiol. 1983;45:1848–53.
Borrel G, Joblin K, Guedon A, Colombet J, Tardy V, Lehours AC, et al. Methanobacterium lacus sp. nov., isolated from the profundal sediment of a freshwater meromictic lake. Int J Syst Evol Microbiol. 2012;62:1625–9.
Krivushin KV, Shcherbakova VA, Petrovskaya LE, Rivkina EM. Methanobacterium veterum sp. nov., from ancient Siberian permafrost. Int J Syst Evol Microbiol. 2010;60:455–9.
Wang Y, Wegener G, Williams TA, Xie R, Hou J, Tian C, et al. A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism. Sci Adv. 2021;7:eabj1453.
Hervé V, Liu P, Dietrich C, Sillam-Dussès D, Stiblik P, Šobotník J, et al. Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites. PeerJ. 2020;8:e8614.
Lind AE, Lewis WH, Spang A, Guy L, Embley TM, Ettema T. Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle. ISME J. 2018;12:2655–67.
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