Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated

Forster P, T. Storelvmo, K. Armour, W. Collins, J.-L. Dufresne, D. Frame, D.J. Lunt, T. Mauritsen, M.D. Palmer, M. Watanabe, M. Wild, and H. Zhang. The Earth’s energy budget, climate feedbacks, and climate sensitivity. Climate Change 2021: The Physical Science Basis Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change. 2021: [Masson-Delmotte, V., P. Zhai, A. Pirani, S.L. Connors, C. Péan, S. Berger, N. Caud, Y. Chen, L. Goldfarb, M.I. Gomis, M. Huang, K. Leitzell, E. Lonnoy, J.B.R. Matthews, T.K. Maycock, T. Waterfield, O. Yelekçi, R. Yu, and B. Zhou (eds.)]. Cambridge University Press. In Press.

IPCC. Climate Change 2021: The Physical Science Basis Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change. 2021:[Masson-Delmotte, V., P. Zhai, A. Pirani, S. L. Connors, C. Péan, S. Berger, N. Caud, Y. Chen, L. Goldfarb, M. I. Gomis, M. Huang, K. Leitzell, E. Lonnoy, J.B.R. Matthews, T. K. Maycock, T. Waterfield, O. Yelekçi, R. Yu and B. Zhou (eds.)]. Cambridge University Press. In Press.

Saunois M, Bousquet P, Poulter B, Peregon A, Ciais P, Canadell JG, et al. The global methane budget 2000–2012. Earth Syst Sci Data. 2016;8(2):697–751.

Article  Google Scholar 

Dangal SRS, Tian H, Zhang B, Pan S, Lu C, Yang J. Methane emission from global livestock sector during 1890–2014: magnitude, trends and spatiotemporal patterns. Glob Chang Biol. 2017;23(10):4147–61.

Article  PubMed  Google Scholar 

Wolf J, Asrar GR, West TO. Revised methane emissions factors and spatially distributed annual carbon fluxes for global livestock. Carbon Balance Manag. 2017;12(1):16.

Article  PubMed  PubMed Central  Google Scholar 

St-Pierre B, Wright AD. Diversity of gut methanogens in herbivorous animals. Animal. 2013;7(Suppl 1):49–56.

Article  PubMed  Google Scholar 

Von Engelhardt W, Wolter S, Lawrenz H, Hemsley J. Production of methane in two non-ruminant herbivores. Comp Biochem Physiol A Physiol. 1978;60(3):309–11.

Article  Google Scholar 

Vendl C, Clauss M, Stewart M, Leggett K, Hummel J, Kreuzer M, et al. Decreasing methane yield with increasing food intake keeps daily methane emissions constant in two foregut fermenting marsupials, the western grey kangaroo and red kangaroo. J Exp Biol. 2015;218(21):3425–34.

Article  PubMed  Google Scholar 

Ouwerkerk D, Maguire A, McMillen L, Klieve A. Hydrogen utilising bacteria from the forestomach of eastern grey (Macropus giganteus) and red (Macropus rufus) kangaroos. Anim Prod Sci. 2009;49(11):1043–51.

Article  CAS  Google Scholar 

Klieve AV, Ouwerkerk D, Maguire AJ. Archaea in the foregut of macropod marsupials: PCR and amplicon sequence-based observations. J Appl Microbiol. 2012;113(5):1065–75.

Article  CAS  PubMed  Google Scholar 

Evans PN, Hinds LA, Sly LI, McSweeney CS, Morrison M, Wright A-DG. Community composition and density of methanogens in the foregut of the tammar wallaby (Macropus eugenii). Appl Environ Microbiol. 2009;75(8):2598.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hoedt EC, Cuív PÓ, Evans PN, Smith WJM, McSweeney CS, Denman SE, et al. Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids. ISME J. 2016;10(10):2376–88.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hoedt EC, Parks DH, Volmer JG, Rosewarne CP, Denman SE, McSweeney CS, et al. Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. ISME J. 2018;12(12):2942–53.

Article  PubMed  PubMed Central  Google Scholar 

Shiffman M, Soo R, Dennis P, Morrison M, Tyson G, Hugenholtz P. Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PeerJ. 2017;5:e4075-e.

Google Scholar 

Thomas CM, Desmond-Le Quéméner E, Gribaldo S, Borrel G. Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom. Nat Commun. 2022;13(1):3358.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Miller TL, Lin C. Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov. Int J Syst Evol Microbiol. 2002;52(Pt 3):819–22.

CAS  PubMed  Google Scholar 

Zhao Y, Boone DR, Mah RA, Boone JE, Xun L. Isolation and characterization of Methanocorpusculum labreanum sp. nov. from the LaBrea Tar Pits. Int J Syst Evol Microbiol. 1989;39(1):10–3.

Google Scholar 

Anderson IJ, Sieprawska-Lupa M, Goltsman E, Lapidus A, Copeland A, Glavina Del Rio T, et al. Complete genome sequence of Methanocorpusculum labreanum type strain Z. Stand Genomic Sci. 2009;1(2):197–203.

Article  PubMed  PubMed Central  Google Scholar 

Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A. 2009;106(45):19126–31.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zellner G, Stackebrandt E, Messner P, Tindall BJ, de Conway ME, Kneifel H, et al. Methanocorpusculaceae fam. nov., represented by Methanocorpusculum parvum, Methanocorpusculum sinense spec. nov. and Methanocorpusculum bavaricum spec. nov. Arch Microbiol. 1989;151(5):381–90.

Article  CAS  PubMed  Google Scholar 

Fernandes KA, Kittelmann S, Rogers CW, Gee EK, Bolwell CF, Bermingham EN, et al. Faecal microbiota of forage-fed horses in New Zealand and the population dynamics of microbial communities following dietary change. PLoS One. 2014;9(11):e112846.

Article  PubMed  PubMed Central  Google Scholar 

Graham DE, White RH. Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics. Nat Prod Rep. 2002;19(2):133–47.

Article  CAS  PubMed  Google Scholar 

Cheeseman P, Toms-Wood A, Wolfe RS. Isolation and properties of a fluorescent compound, factor 420, from Methanobacterium strain M.o.H. J Bacteriol. 1972;112(1):527–31.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nayfach S, Shi ZJ, Seshadri R, Pollard KS, Kyrpides NC. New insights from uncultivated genomes of the global human gut microbiome. Nature. 2019;568(7753):505–10.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol. 2017;2(11):1533–42.

Article  CAS  PubMed  Google Scholar 

Xie F, Jin W, Si H, Yuan Y, Tao Y, Liu J, et al. An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants. Microbiome. 2021;9(1):137.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gilroy R, Ravi A, Getino M, Pursley I, Horton DL, Alikhan NF, et al. Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ. 2021;9:e10941.

Article  PubMed  PubMed Central  Google Scholar 

Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2019;36(6):1925–7.

PubMed  PubMed Central  Google Scholar 

Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3):e9490.

Article  PubMed  PubMed Central  Google Scholar 

Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep. 2016;6(1):24373.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gilmore SP, Henske JK, Sexton JA, Solomon KV, Seppala S, Yoo JI, et al. Genomic analysis of methanogenic archaea reveals a shift towards energy conservation. BMC Genomics. 2017;18(1):639.

Article  PubMed  PubMed Central  Google Scholar 

Médici R, Stammes H, Kwakernaak S, Otten LG, Hanefeld U. Assessing the stereoselectivity of Serratia marcescens CECT 977 2,3-butanediol dehydrogenase. Catalysis Sci Technol. 2017;7(9):1831–7.

Article  Google Scholar 

Kotani T, Yamamoto T, Yurimoto H, Sakai Y, Kato N. Propane monooxygenase and NAD+-dependent secondary alcohol dehydrogenase in propane metabolism by Gordonia sp. Strain TY-5. J Bacteriol. 2003;185(24):7120–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schweiger G, Dutscho R, Buckel W. Purification of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. An iron-sulfur protein. Eur J Biochem. 1987;169(2):441–8.

Article  CAS  PubMed  Google Scholar 

Porter AW, Young LY. Chapter five - Benzoyl-CoA, a universal biomarker for anaerobic degradation of aromatic compounds. In: Sariaslani S, Gadd GM, editors. Advances in Applied Microbiology. 88: Academic Press; 2014. p. 167–203.

Google Scholar 

Najmudin S, Guerreiro CIPD, Carvalho AL, Prates JAM, Correia MAS, Alves VD, et al. Xyloglucan is recognized by carbohydrate-binding modules that interact with β-glucan chains*. J Biol Chem. 2006;281(13):8815–28.

Article  CAS  PubMed  Google Scholar 

Zellner G, Alten C, Stackebrandt E, de Conway ME, Winter J. Isolation and characterization of Methanocorpusculum parvum, gen. nov., spec. nov., a new tungsten requiring, coccoid methanogen. Arch Microbiol. 1987;147(1):13–20.

Article  CAS  Google Scholar 

Hong P-Y, Wheeler E, Cann IKO, Mackie RI. Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing. ISME J. 2011;5(9):1461–70.

Article  PubMed 

留言 (0)

沒有登入
gif