Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis |…

Hackstein JH, Stumm CK. Methane production in terrestrial arthropods. Proc Natl Acad Sci USA. 1994;91:54415.

CAS PubMed PubMed Central Article Google Scholar

Hackstein JHP, van Alen TA. Fecal methanogens and vertebrate evolution. Evolution. 1996;50:55972.

PubMed Article PubMed Central Google Scholar

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.

CAS PubMed PubMed Central Article Google Scholar

Raymann K, Moeller AH, Goodman AL, Ochman H. Unexplored archaeal diversity in the great ape gut microbiome. mSphere. 2017;2:e00026-17.

PubMed PubMed Central Article Google Scholar

Douglas AE. Multiorganismal insects: diversity and function of resident microorganisms. Annu Rev Entomol. 2015;60:1734.

CAS PubMed Article Google Scholar

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.

CAS PubMed PubMed Central Article Google Scholar

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.

CAS PubMed PubMed Central Article Google Scholar

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.

PubMed PubMed Central Article CAS Google Scholar

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.

PubMed PubMed Central Article CAS Google Scholar

Borrel G, Brugre JF, Gribaldo S, Schmitz RA, Moissl-Eichinger C. The host-associated archaeome. Nat Rev Microbiol. 2020;18:62236.

CAS PubMed Article Google Scholar

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.

CAS PubMed Article Google Scholar

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.

CAS PubMed Article Google Scholar

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.

PubMed PubMed Central Article CAS Google Scholar

Brune, A. Methanogens in the digestive tract of termites. In: Hackstein JHP, editor. (Endo)symbiotic methanogenic archaea. Berlin: Springer; 2018. p. 81101.

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.

PubMed PubMed Central Article Google Scholar

Sprenger WW, Hackstein JHP, Keltjens JT. The energy metabolism of Methanomicrococcus blatticola: physiological and biochemical aspects. Antonie van Leeuwenhoek. 2005;87:28999.

CAS PubMed Article Google Scholar

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.

CAS PubMed Article Google Scholar

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.

CAS PubMed PubMed Central Article Google Scholar

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.

CAS PubMed PubMed Central Article Google Scholar

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.

CAS PubMed PubMed Central Article Google Scholar

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.

CAS PubMed Article Google Scholar

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.

CAS PubMed PubMed Central Article Google Scholar

Sllinger A, Urich T. Methylotrophic methanogens everywherephysiology and ecology of novel players in global methane cycling. Biochem Soc Trans. 2019;47:1895907.

PubMed Article Google Scholar

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.

CAS PubMed PubMed Central Article Google Scholar

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.

PubMed PubMed Central Article CAS Google Scholar

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.

CAS PubMed Article Google Scholar

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.

CAS PubMed Article Google Scholar

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.

Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res. 2003;31:3713.

CAS PubMed PubMed Central Article Google Scholar

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.

CAS Article Google Scholar

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.

CAS PubMed PubMed Central Article Google Scholar

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.

CAS PubMed PubMed Central Article Google Scholar

Coutinho PM, Deleury E, Davies GJ, Henrissat B. An evolving hierarchical family classification for glycosyltransferases. J Mol Biol. 2003;328:30717.

CAS PubMed Article Google Scholar

Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2014;2:e243.

PubMed PubMed Central Article Google Scholar

Johnson LS, Eddy SR, Portugaly E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics. 2010;11:431.

PubMed PubMed Central Article CAS Google Scholar

Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:77280.

CAS PubMed PubMed Central Article Google Scholar

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.

PubMed PubMed Central Article CAS Google Scholar

Lartillot N, Lepage T, Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics. 2009;25:22868.

CAS PubMed Article PubMed Central Google Scholar

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.

CAS PubMed Article Google Scholar

Miele V, Penel S, Duret L. Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics. 2011;12:116.

PubMed PubMed Central Article Google Scholar

Csurs, M. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics. 2010;26:19102.

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.

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.

CAS PubMed PubMed Central Article Google Scholar

Haft DH, Payne SH, Selengut JD. Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. J Bacteriol. 2012;194:3648.

CAS PubMed PubMed Central Article Google Scholar

Porter NT, Martens EC. The critical roles of polysaccharides in gut microbial ecology and physiology. Annu Rev Microbiol. 2017;71:34969.

CAS PubMed Article Google Scholar

Albers SV, Meyer BH. The archaeal cell envelope. Nat Rev Microbiol. 2011;9:41426.

CAS PubMed Article Google Scholar

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.

CAS PubMed Article Google Scholar

Morita, RY. Bacteria in oligotrophic environments. New York, NY: Chapman & Hall; 1997.

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.

PubMed PubMed Central Article CAS Google Scholar

Harris RM, Webb DC, Howitt SM, Cox GB. Characterization of PitA and PitB from Escherichia coli. J Bacteriol. 2001;183:500814.

CAS PubMed PubMed Central Article Google Scholar

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.

Article CAS Google Scholar

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.

PubMed PubMed Central Article CAS Google Scholar

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.

The rest is here:
Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis |...