{"id":1028168,"date":"2021-09-10T05:27:52","date_gmt":"2021-09-10T09:27:52","guid":{"rendered":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/uncategorized\/comparative-genomic-analysis-of-methanimicrococcus-blatticola-provides-insights-into-host-adaptation-in-archaea-and-the-evolution-of-methanogenesis\/"},"modified":"2021-09-10T05:27:52","modified_gmt":"2021-09-10T09:27:52","slug":"comparative-genomic-analysis-of-methanimicrococcus-blatticola-provides-insights-into-host-adaptation-in-archaea-and-the-evolution-of-methanogenesis","status":"publish","type":"post","link":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/genome\/comparative-genomic-analysis-of-methanimicrococcus-blatticola-provides-insights-into-host-adaptation-in-archaea-and-the-evolution-of-methanogenesis\/","title":{"rendered":"Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis |&#8230;"},"content":{"rendered":"<p><p>Hackstein JH, Stumm CK. Methane production in terrestrial arthropods. Proc Natl Acad Sci USA. 1994;91:54415.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Hackstein JHP, van Alen TA. Fecal methanogens and vertebrate evolution. Evolution. 1996;50:55972.<\/p>\n<p>PubMed    Article    PubMed Central                        Google Scholar                <\/p>\n<p>Borrel G, McCann A, Deane J, Neto MC, Lynch DB, Brugre JF, et al. Genomics and metagenomics of trimethylamine-utilizing archaea in the human gut microbiome. ISME J. 2017;11:205974.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Raymann K, Moeller AH, Goodman AL, Ochman H. Unexplored archaeal diversity in the great ape gut microbiome. mSphere. 2017;2:e00026-17.<\/p>\n<p>PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Douglas AE. Multiorganismal insects: diversity and function of resident microorganisms. Annu Rev Entomol. 2015;60:1734.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>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;104:106438.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Gaci N, Borrel G, Tottey W, O'Toole PW, Brugre JF. Archaea and the human gut: new beginning of an old story. World J Gastroenterol. 2014;20:1606278.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>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.<\/p>\n<p>PubMed    PubMed Central    Article    CAS                        Google Scholar                <\/p>\n<p>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;81:133852.<\/p>\n<p>PubMed    PubMed Central    Article    CAS                        Google Scholar                <\/p>\n<p>Borrel G, Brugre JF, Gribaldo S, Schmitz RA, Moissl-Eichinger C. The host-associated archaeome. Nat Rev Microbiol. 2020;18:62236.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>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;50:198999.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Jarvis GN, Strmpl C, Burgess DM, Skillman LC, Moore ER, Joblin KN. Isolation and identification of ruminal methanogens from grazing cattle. Curr Microbiol. 2000;40:32732.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>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.<\/p>\n<p>PubMed    PubMed Central    Article    CAS                        Google Scholar                <\/p>\n<p>Brune, A. Methanogens in the digestive tract of termites. In: Hackstein JHP, editor. (Endo)symbiotic methanogenic archaea. Berlin: Springer; 2018. p. 81101.<\/p>\n<p>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.<\/p>\n<p>PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Sprenger WW, Hackstein JHP, Keltjens JT. The energy metabolism of Methanomicrococcus blatticola: physiological and biochemical aspects. Antonie van Leeuwenhoek. 2005;87:28999.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>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;60:26675.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Borrel G, Adam PS, McKay LJ, Chen LX, Sierra-Garca IN, Sieber C, et al. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nat Microbiol. 2019;4:60313.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>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;10:247887.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>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.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>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.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Borrel G, O'Toole PW, Harris HM, Peyret P, Brugre JF, Gribaldo S. Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis. Genome Biol Evol. 2013;5:176980.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Sllinger A, Urich T. Methylotrophic methanogens everywherephysiology and ecology of novel players in global methane cycling. Biochem Soc Trans. 2019;47:1895907.<\/p>\n<p>PubMed    Article                        Google Scholar                <\/p>\n<p>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;19:45577.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>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.<\/p>\n<p>PubMed    PubMed Central    Article    CAS                        Google Scholar                <\/p>\n<p>Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol. 2016;428:72631.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Huerta-Cepas J, Szklarczyk D, Heller D, Hernndez-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:D30914.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>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:D42732.<\/p>\n<p>Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res. 2003;31:3713.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>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;305:56780.<\/p>\n<p>CAS    Article                        Google Scholar                <\/p>\n<p>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;25:104355.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>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:W95101.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Coutinho PM, Deleury E, Davies GJ, Henrissat B. An evolving hierarchical family classification for glycosyltransferases. J Mol Biol. 2003;328:30717.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2014;2:e243.<\/p>\n<p>PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Johnson LS, Eddy SR, Portugaly E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics. 2010;11:431.<\/p>\n<p>PubMed    PubMed Central    Article    CAS                        Google Scholar                <\/p>\n<p>Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:77280.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>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.<\/p>\n<p>PubMed    PubMed Central    Article    CAS                        Google Scholar                <\/p>\n<p>Lartillot N, Lepage T, Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics. 2009;25:22868.<\/p>\n<p>CAS    PubMed    Article    PubMed Central                        Google Scholar                <\/p>\n<p>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;32:26874.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Miele V, Penel S, Duret L. Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics. 2011;12:116.<\/p>\n<p>PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Csurs, M. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics. 2010;26:19102.<\/p>\n<p>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. 25981.<\/p>\n<p>Ebbes M, Bleymller WM, Cernescu M, Nlker R, Brutschy B, Niemann HH. Fold and function of the InlB B-repeat. J Biol Chem. 2011;286:15496506.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Haft DH, Payne SH, Selengut JD. Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. J Bacteriol. 2012;194:3648.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>Porter NT, Martens EC. The critical roles of polysaccharides in gut microbial ecology and physiology. Annu Rev Microbiol. 2017;71:34969.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Albers SV, Meyer BH. The archaeal cell envelope. Nat Rev Microbiol. 2011;9:41426.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>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;3:37987.<\/p>\n<p>CAS    PubMed    Article                        Google Scholar                <\/p>\n<p>Morita, RY. Bacteria in oligotrophic environments. New York, NY: Chapman & Hall; 1997.<\/p>\n<p>Paula FS, Chin JP, Schnrer A, Mller 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.<\/p>\n<p>PubMed    PubMed Central    Article    CAS                        Google Scholar                <\/p>\n<p>Harris RM, Webb DC, Howitt SM, Cox GB. Characterization of PitA and PitB from Escherichia coli. J Bacteriol. 2001;183:500814.<\/p>\n<p>CAS    PubMed    PubMed Central    Article                        Google Scholar                <\/p>\n<p>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.<\/p>\n<p>Article    CAS                        Google Scholar                <\/p>\n<p>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.<\/p>\n<p>PubMed    PubMed Central    Article    CAS                        Google Scholar                <\/p>\n<p>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.<\/p>\n<p><!-- Auto Generated --><\/p>\n<p>The rest is here:<br \/>\n<a target=\"_blank\" href=\"https:\/\/www.nature.com\/articles\/s43705-021-00050-y\" title=\"Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis |...\" rel=\"noopener\">Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis |...<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p> Hackstein JH, Stumm CK. Methane production in terrestrial arthropods.  <a href=\"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/genome\/comparative-genomic-analysis-of-methanimicrococcus-blatticola-provides-insights-into-host-adaptation-in-archaea-and-the-evolution-of-methanogenesis\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":9,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[25],"tags":[],"class_list":["post-1028168","post","type-post","status-publish","format-standard","hentry","category-genome"],"_links":{"self":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/1028168"}],"collection":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/users\/9"}],"replies":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/comments?post=1028168"}],"version-history":[{"count":0,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/1028168\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/media?parent=1028168"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/categories?post=1028168"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/tags?post=1028168"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}