The Complete genome sequence of Methanobrevibacter sp. ABM4

Standards in Genomic Sciences

Volumn 8, Issue 2, 2013, Pages 215-227

  Leahy, S C ^a,b   Kelly, W J ^b   Li, D ^a,b   Li, Y ^a,b   Altermann, E ^b   Lambie, S C ^b   Cox, F ^b   Attwood, G T ^a,b  

^a New Zealand Agricultural Greenhouse Gas Research Centre   (New Zealand)

^b AGRESEARCH GRASSLANDS   (New Zealand)

Author keywords

Methane; Methanobrevibacter; Methanogen; Ruminant

Indexed keywords

DNA DIRECTED RNA POLYMERASE;

ARTICLE; BACTERIAL GROWTH; DNA ISOLATION; ELECTRON MICROSCOPY; GENE SEQUENCE; METHANOBREVIBACTER; METHANOGENESIS; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PULSED FIELD GEL ELECTROPHORESIS; SEQUENCE ALIGNMENT;

METHANOBREVIBACTER; METHANOBREVIBACTER RUMINANTIUM; METHANOBREVIBACTER SP.; METHANOBREVIBACTER WOLINII; OVIS ARIES;

EID: 84879355108     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.3977691     Document Type: Article

References (53)

1. Janssen PH, Kirs M. Structure of the archaeal community of the rumen. Appl Environ Microbiol 2008; 74:3619-3625.PubMed, http://dx.doi.org/10.1128/AEM.02812-07
2. Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, Li D, Kong Z, McTavish S, Sang C, 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. http://dx.doi.org/10.1371/journal.pone.0008926
3. Wedlock N, Janssen PH, Leahy S, Shu D, Buddle BM. Progress in the development of vaccines against rumen methanogens. Animal 2013; SUPPL 2:244-252. http://dx.doi.org/10.1017/S1751731113000682
4. Leahy SC, Kelly WJ, Ronimus RS, Wedlock N, Altermann E, Attwood GT. Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies. Animal 2013; SUPPL 2:235-243. http://dx.doi.org/10.1017/S1751731113000700
5. Simcock DC, Joblin KN, Scott I, Burgess DM, Rogers CW, Pomroy WE, Simpson HV. Hypergastrinaemia, abomasal bacterial population densities and pH in sheep infected with Ostertagia circumcincta. Int J Parasitol 1999; 29:1053-1063. PubMed. http://dx.doi.org/10.1016/S0020-7519(99)00065- X
6. Bruno WJ, Socci ND, Halpern AL. Weighted Neighbor Joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol Biol Evol 2000; 17:189-197. PubMed http://dx.doi.org/10.1093/oxfordjournals.molbev.a 026231
7. Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed- Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 2007; 35:D169-D172. PubMed http://dx.doi.org/10.1093/nar/gkl889
8. Yu Z, Garcia-Gonzalez R, Schanbacher F, Morrison M. Evaluations of different hypervariable regions of archaeal 16S rRNA genes in profiling of methanogens by archaea-specific PCR and denaturing gradient gel electrophoresis. Appl Environ Microbiol 2008; 74:889-893. PubMed http://dx.doi.org/10.1128/AEM.00684-07
9. Zhou M, Hernandez-Sanabria E, Guan LL. Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. Appl Environ Microbiol 2009; 75:6524-6533. PubMed. http://dx.doi.org/10.1128/AEM.02815-08
10. Zhou M, Hernandez-Sanabria E, Guan Le L. Characterization of variation in rumen methanogenic communities under different dietary and host feed efficiency conditions, as determined by PCR-denaturing gradient gel electrophoresis analysis. Appl Environ Microbiol 2010; 76:3776-3786. PubMed http://dx.doi.org/10.1128/AEM.00010-10
11. Wright ADG, Ma X, Obispo NE. Methanobrevibacter phylotypes are the dominant methanogens in sheep from Venezuela. Microb Ecol 2008; 56:390-394. PubMed http://dx.doi.org/10.1007/s00248-007-9351-x
12. Williams YJ, Popovski S, Rea SM, Skillman LC, Toovey AF, Northwood KS, Wright ADG. A vaccine against rumen methanogens can alter the composition of archaeal populations. Appl Environ Microbiol 2009; 75:1860-1866. PubMed http://dx.doi.org/10.1128/AEM.02453-08
13. St-Pierre B, Wright AD. Molecular analysis of methanogenic archeaa in the forestomach of the alpaca (Vicugna pacos). BMC Microbiol 2012; 12:1-12. PubMed http://dx.doi.org/10.1186/1471 - 2180-12-1
14. King EE, Smith RP, St-Pierre B, Wright AD. Differences in rumen methanogen populations of lac- tating Jersey and Holstein dairy cows under the same diet regimen. Appl Environ Microbiol 2011; 77:5682-5687. PubMed. http://dx.doi.org/10.1128/AEM.05130-11
15. 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; 52:819-822. PubMed http://dx.doi.org/10.1099/ijs.0.02022-0
16. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
17. Garrity GM, Holt JG. Phylum AII. Euryarchaeota phy. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 211-355.
18. Validation List no. 85. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2002; 52:685-690. PubMed http://dx.doi.org/10.1099/ijs.0.02358-0
19. Boone DR. Class I. Methanobacteria class. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 213.
20. List Editor. Validation List no. 6. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol 1981; 31:215-218. http://dx.doi.org/10.1099/00207713-31-2-215
21. Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. Methanogens: reevaluation of a unique biological group. Microbiol Rev 1979; 43:260-296. PubMed
22. Judicial Commission of the International Committee on Systematics of Prokaryotes. The nomencla- tural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79. Int J Syst Evol Microbiol 2005; 55:517-518. PubMed http://dx.doi.org/10.1099/ijs.0.63548-0
23. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420. http://dx.doi.org/10.1099/00207713-30-1-225
24. Barker HA. Bacterial Fermentations, John Wiley and Sons, New York, 1956, p. 15.
25. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25-29. PubMed http://dx.doi.org/10.1038/75556
26. Joblin KN, Naylor GE, Williams AG. Effect of Methanobrevibacter smithii on xylanolytic activity of anaerobic ruminal fungi. Appl Environ Microbiol 1990; 56:2287-2295.PubMed
27. Widdel F, Kohring G, Mayer F. Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids III. Characterization of the filamentous gliding Desulfonema limicola gen. nov. sp. nov., and Desulfonema magnum sp. nov. Arch Microbiol 1983; 134:286-294. http://dx.doi.org/10.1007/BF00407804
28. Tschech A, Pfennig N. Growth yield increase linked to caffeate reduction in Acetobacterium woodii. Arch Microbiol 1984; 137:163-167. http://dx.doi.org/10.1007/BF00414460
29. Jarrell KF, Faguy D, Herbert AM, Kalmakoff ML. A general method of isolating high molecular weight DNA from methanogenic archaea (archaebacteria). Can J Microbiol 1992; 38:65-68.PubMed http://dx.doi.org/10.1139/m92-010
30. Staden R, Beal KF, Bonfield JK. The Staden package, 1998. Methods Mol Biol 2000; 132:115-130.PubMed
31. Altermann E, Klaenhammer T. GAMOLA: a new local solution for sequence annotation and analyzing draft and finished prokaryotic genomes. OMICS 2003; 7:161-169.PubMed http://dx.doi.org/10.1089/153623103322246557
32. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Ranjandream MA, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000; 16:944-945. PubMed http://dx.doi.org/10.1093/bioinformatics/16.10.94
33. Delcher AL, Harmon D, Kasif S, White O, Salzberg S. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999; 27: 4636-4641. PubMed http://dx.doi.org/10.1093/nar/27.23.4636.
34. Altschul SF, Gish W, Miller W, Myers E, Lipman D. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. PubMed
35. Gish W, States D. Identification of protein coding regions by database similarity search. Nat Genet 1993; 3:266-272. PubMed http://dx.doi.org/10.1038/ng0393-266
36. NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2013; 41:D8-D20. PubMed http://dx.doi.org/10.1093/nar/gks1189
37. Tatusov RL, Galperin M, Natale D, Koonin E. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33-36.PubMed http://dx.doi.org/10.1093/nar/28.1.33
38. Eddy SR. Profile hidden Markov models. Bioinformatics 1998; 14:755-763PubMed http://dx.doi.org/10.1093/bioinformatics/14.9.755
39. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, et al. The Pfam protein families database. Nucleic Acids Res 2012; 40:D290-D301.PubMed http://dx.doi.org/10.1093/nar/gkr1065
40. Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E. TIGRFAMs and Genome Properties in 2013. Nucleic Acids Res 2013; 41:D387-D395. PubMed. http://dx.doi.org/10.1093/nar/gks1234
41. Krogh A, Larsson B, von Heijne G, Sonnhammer D. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567-580. PubMed. http://dx.doi.org/10.1006/jmbi.2000.4315, http://www.cbs.dtu.dk/services/TMHMM/
42. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011; 8:785-786. PubMed. http://dx.doi.org/10.1038/nmeth.1701
43. Lowe TM, Eddy S. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955-964. PubMed
44. Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A. Rfam 11.0: 10 years of RNA families. Nucleic Ac ids Res 2013; 41:D226-D232. PubMed. http://dx.doi.org/10.1093/nar/gks1005
45. Eddy SR. A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics 2002; 3:18. PubMed. http://dx.doi.org/10.1186/1471-2105-3-18
46. Benson DA, Cavanaugh M, Clark K, Karsch- Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2013; 41:D36-D42. PubMed. http://dx.doi.org/10.1093/nar/gks1195
47. Lee JH, Rhee MS, Kumar S, Lee GH, Chang DH, Kim DS, Choi SH, Lee DW, Yoon MH, Kim BC. Genome sequence of Methanobrevibacter sp. strain JH1, isolated from rumen of Korean native cattle. Genome Announc 2013; 1:e00002- e00013. PubMed
48. Samuel BS, Hansen E, Manchester J, Coutinho P, Henrissat B, Fulton R, Latreille P, Kim K, Wilson RK, Gordon JI. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci USA 2007; 104:10643-10648. PubMed. http://dx.doi.org/10.1073/pnas.0704189104
49. Fricke WF, Seedorf H, Henne A, Kruer M, Liesegang H, Hedderich R, Gottschalk G, Thauer RK. 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; 188:642-658. PubMed. http://dx.doi.org/10.112 8/IB.188.2.642-658.2006
50. Li L, Stoeckert CJ, Jr., Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178-2189.PubMed. http://dx.doi.org/10.1101/gr.1224503
51. Reeve JN, Nolling J, Morgan RM, Smith DR. Methanogenesis: genes, genomes, and who's on first? J Bacteriol 1997; 179:5975-5986. PubMed
52. Berk H, Thauer RK. Function of coenzyme F420- dependent NADP reductase in methanogenic archaea containing an NADP-dependent alcohol dehydrogenase. Arch Microbiol 1997; 168:396-402. PubMed. http://dx.doi.org/10.1007/s002030050514
53. Brochier C, Forterre P, Gribaldo S. Archaeal phy- logeny based on proteins of the transcription and translation: tackling the Methanopyrus kandleri paradox. Genome Biol2004; 5:R17. PubMed http://dx.doi.org/10.1186/gb-2004-5-3-r17