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Volumn 6, Issue 2, 2012, Pages 430-439

A 'universal' type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities

Author keywords

16S rRNA gene; Archaea; chaperonin; rumen; thermosome; universal PCR

Indexed keywords

CHAPERONIN; RNA 16S;

EID: 84855972666     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2011.96     Document Type: Article
Times cited : (24)

References (45)
  • 2
    • 42349115395 scopus 로고    scopus 로고
    • Value of recN sequences for species identification and as a phylogenetic marker within the family "Leuconostocaceae"
    • DOI 10.2436/20.1501.01.42
    • Arahal DR, Sanchez E, Macian MC, Garay E. (2008). Value of recN sequences for species identification and as a phylogenetic marker within the family 'Leuconostocaceae'. Int Microbiol 11: 33-39. (Pubitemid 351556378)
    • (2008) International Microbiology , vol.11 , Issue.1 , pp. 33-39
    • Arahal, D.R.1    Sanchez, E.2    Macian, M.C.3    Garay, E.4
  • 3
    • 0033598189 scopus 로고    scopus 로고
    • Recurrent paralogy in the evolution of archaeal chaperonins
    • DOI 10.1016/S0960-9822(99)80457-6
    • Archibald JM, Logsdon JM, Doolittle WF. (1999). Recurrent paralogy in the evolution of archaeal chaperonins. Curr Biol 9: 1053-1056. (Pubitemid 29456177)
    • (1999) Current Biology , vol.9 , Issue.18 , pp. 1053-1056
    • Archibald, J.M.1    Logsdon Jr., J.M.2    Doolittle, W.F.3
  • 4
    • 0242384034 scopus 로고    scopus 로고
    • Review and re-analysis of domain-specific 16S primers
    • DOI 10.1016/j.mimet.2003.08.009
    • Baker GC, Smith JJ, Cowan DA. (2003). Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55: 541-555. (Pubitemid 37357207)
    • (2003) Journal of Microbiological Methods , vol.55 , Issue.3 , pp. 541-555
    • Baker, G.C.1    Smith, J.J.2    Cowan, D.A.3
  • 5
    • 33744483524 scopus 로고    scopus 로고
    • Archaeal habitats- from the extreme to the ordinary
    • Chaban B, Ng SY, Jarrell KF. (2006). Archaeal habitats- from the extreme to the ordinary. Can J Microbiol 52: 73-116.
    • (2006) Can J Microbiol , vol.52 , pp. 73-116
    • Chaban, B.1    Ng, S.Y.2    Jarrell, K.F.3
  • 6
    • 58149200948 scopus 로고    scopus 로고
    • The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis
    • Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ et al. (2009). The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
    • (2009) Nucleic Acids Res , vol.37
    • Cole, J.R.1    Wang, Q.2    Cardenas, E.3    Fish, J.4    Chai, B.5    Farris, R.J.6
  • 7
    • 35948938623 scopus 로고    scopus 로고
    • Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane
    • DOI 10.1111/j.1574-6941.2007.00394.x
    • Denman SE, Tomkins NW, McSweeney CS. (2007). Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane. FEMS Microbiol Ecol 62: 313-322. (Pubitemid 350076062)
    • (2007) FEMS Microbiology Ecology , vol.62 , Issue.3 , pp. 313-322
    • Denman, S.E.1    Tomkins, N.W.2    McSweeney, C.S.3
  • 9
    • 29044443396 scopus 로고    scopus 로고
    • Enumeration of specific bacterial populations in complex intestinal communities using quantitative PCR based on the chaperonin-60 target
    • DOI 10.1016/j.mimet.2005.04.006, PII S0167701205001235
    • Dumonceaux TJ, Hill JE, Briggs SA, Amoako KK, Hemmingsen SM, Van Kessel AG. (2006a). Enumeration of specific bacterial populations in complex intestinal communities using quantitative PCR based on the chaperonin-60 target. J Microbiol Methods 64: 46-62. (Pubitemid 41790486)
    • (2006) Journal of Microbiological Methods , vol.64 , Issue.1 , pp. 46-62
    • Dumonceaux, T.J.1    Hill, J.E.2    Briggs, S.A.3    Amoako, K.K.4    Hemmingsen, S.M.5    Van Kessel, A.G.6
  • 10
    • 33646112924 scopus 로고    scopus 로고
    • Characterization of intestinal microbiota and response to dietary virginiamycin supplementation in the broiler chicken
    • Dumonceaux TJ, Hill JE, Hemmingsen SM, Van Kessel AG. (2006b). Characterization of intestinal microbiota and response to dietary virginiamycin supplementation in the broiler chicken. Appl Environ Microbiol 72: 2815-2823.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 2815-2823
    • Dumonceaux, T.J.1    Hill, J.E.2    Hemmingsen, S.M.3    Van Kessel, A.G.4
  • 11
    • 0000122573 scopus 로고
    • PHYLIP-phylogeny inference package (version 3.2
    • Felsenstein J. (1989). PHYLIP-phylogeny inference package (version 3.2). Cladistics 5: 164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 12
    • 0018974560 scopus 로고
    • The phylogeny of prokaryotes
    • Fox GE, Stackebrandt E, Hespell RB, Gibson J, Maniloff J, Dyer TA et al. (1980). The phylogeny of prokaryotes. Science 209: 457-463. (Pubitemid 10022749)
    • (1980) Science , vol.209 , Issue.4455 , pp. 457-463
    • Fox, G.E.1    Stackebrandt, E.2    Hespell, R.B.3
  • 13
    • 70350515921 scopus 로고    scopus 로고
    • Partial sequence comparison of the rpoB, sodA, groEL and gyrB genes within the genus Streptococcus
    • Glazunova OO, Raoult D, Roux V. (2009). Partial sequence comparison of the rpoB, sodA, groEL and gyrB genes within the genus Streptococcus. Int J Syst Evol Microbiol 59: 2317-2322.
    • (2009) Int J Syst Evol Microbiol , vol.59 , pp. 2317-2322
    • Glazunova, O.O.1    Raoult, D.2    Roux, V.3
  • 15
    • 33645463746 scopus 로고    scopus 로고
    • Identification of Campylobacter spp. and discrimination from Helicobacter and Arcobacter spp. by direct sequencing of PCR-amplified cpn60 sequences and comparison to cpnDB, a chaperonin reference sequence database
    • Hill JE, Paccagnella A, Law K, Melito PL, Woodward DL, Price L et al. (2006a). Identification of Campylobacter spp. and discrimination from Helicobacter and Arcobacter spp. by direct sequencing of PCR-amplified cpn60 sequences and comparison to cpnDB, a chaperonin reference sequence database. J Med Microbiol 55: 393-399.
    • (2006) J Med Microbiol , vol.55 , pp. 393-399
    • Hill, J.E.1    Paccagnella, A.2    Law, K.3    Melito, P.L.4    Woodward, D.L.5    Price, L.6
  • 17
    • 33644840902 scopus 로고    scopus 로고
    • Improved template representation in cpn 60 polymerase chain reaction (PCR) product libraries generated from complex templates by application of a specific mixture of PCR primers
    • DOI 10.1111/j.1462-2920.2005.00944.x
    • Hill JE, Town JR, Hemmingsen SM. (2006b). Improved template representation in cpn60 polymerase chain reaction (PCR) product libraries generated from complex templates by application of a specific mixture of PCR primers. Environ Microbiol 8: 741-746. (Pubitemid 43363330)
    • (2006) Environmental Microbiology , vol.8 , Issue.4 , pp. 741-746
    • Hill, J.E.1    Town, J.R.2    Hemmingsen, S.M.3
  • 18
    • 0037052320 scopus 로고    scopus 로고
    • Isolating "uncultivabte" microorganisms in pure culture in a simulated natural environment
    • DOI 10.1126/science.1070633
    • Kaeberlein T, Lewis K, Epstein SS. (2002). Isolating 'uncultivable' microorganisms in pure culture in a simulated natural environment. Science 296: 1127-1129. (Pubitemid 34517131)
    • (2002) Science , vol.296 , Issue.5570 , pp. 1127-1129
    • Kaeberlein, T.1    Lewis, K.2    Epstein, S.S.3
  • 19
    • 0029062216 scopus 로고
    • The chaperonin containing t-complex polypeptide 1 (TCP-1). Multisubunit machinery assisting in protein folding and assembly in the eukaryotic cytosol
    • Kubota H, Hynes G, Willison K. (1995). The chaperonin containing t-complex polypeptide 1 (TCP-1). Multisubunit machinery assisting in protein folding and assembly in the eukaryotic cytosol. Eur J Biochem 230: 3-16.
    • (1995) Eur J Biochem , vol.230 , pp. 3-16
    • Kubota, H.1    Hynes, G.2    Willison, K.3
  • 21
    • 63849276112 scopus 로고    scopus 로고
    • Archaeal chaperonins
    • Large AT, Lund PA. (2009). Archaeal chaperonins. Front Biosci 14: 1304-1324.
    • (2009) Front Biosci , vol.14 , pp. 1304-1324
    • Large, A.T.1    Lund, P.A.2
  • 22
    • 0036856362 scopus 로고    scopus 로고
    • The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill
    • Luton PE, Wayne JM, Sharp RJ, Riley PW. (2002). The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148: 3521-3530. (Pubitemid 35414462)
    • (2002) Microbiology , vol.148 , Issue.11 , pp. 3521-3530
    • Luton, P.E.1    Wayne, J.M.2    Sharp, R.J.3    Riley, P.W.4
  • 25
    • 52349091138 scopus 로고    scopus 로고
    • A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene
    • Mihajlovski A, Alric M, Brugere JF. (2008). A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene. Res Microbiol 159: 516-521.
    • (2008) Res Microbiol , vol.159 , pp. 516-521
    • Mihajlovski, A.1    Alric, M.2    Brugere, J.F.3
  • 26
    • 65549111754 scopus 로고    scopus 로고
    • Infernal 1.0: Inference of RNA alignments
    • Nawrocki EP, Kolbe DL, Eddy SR. (2009). Infernal 1.0: Inference of RNA alignments. Bioinformatics 25: 1335-1337.
    • (2009) Bioinformatics , vol.25 , pp. 1335-1337
    • Nawrocki, E.P.1    Kolbe, D.L.2    Eddy, S.R.3
  • 28
    • 0030203863 scopus 로고    scopus 로고
    • TreeView: An application to display phylogenetic trees on personal computers
    • Page RD. (1996). TreeView: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358.
    • (1996) Comput Appl Biosci , vol.12 , pp. 357-358
    • Page, R.D.1
  • 29
    • 3042826875 scopus 로고    scopus 로고
    • Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins
    • DOI 10.1111/j.1462-2920.2004.00617.x
    • Santos SR, Ochman H. (2004). Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol 6: 754-759. (Pubitemid 38847740)
    • (2004) Environmental Microbiology , vol.6 , Issue.7 , pp. 754-759
    • Santos, S.R.1    Ochman, H.2
  • 30
    • 65549089957 scopus 로고    scopus 로고
    • Pyrosequencing of the chaperonin-60 universal target as a tool for determining microbial community composition
    • Schellenberg J, Links MG, Hill JE, Dumonceaux TJ, Peters GA, Tyler S et al. (2009). Pyrosequencing of the chaperonin-60 universal target as a tool for determining microbial community composition. Appl Environ Microbiol 75: 2889-2898.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 2889-2898
    • Schellenberg, J.1    Links, M.G.2    Hill, J.E.3    Dumonceaux, T.J.4    Peters, G.A.5    Tyler, S.6
  • 33
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • DOI 10.1093/nar/25.24.4876
    • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. (1997). The CLUSTAL-X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882. (Pubitemid 28022245)
    • (1997) Nucleic Acids Research , vol.25 , Issue.24 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 34
    • 0025748752 scopus 로고
    • A molecular chaperone from a thermophilic archaebacterium is related to the eukaryotic protein t-complex polypeptide-1
    • Trent JD, Nimmesgern E, Wall JS, Hartl FU, Horwich AL. (1991). A molecular chaperone from a thermophilic archaebacterium is related to the eukaryotic protein t-complex polypeptide-1. Nature 354: 490-493. (Pubitemid 21896866)
    • (1991) Nature , vol.354 , Issue.6353 , pp. 490-493
    • Trent, J.D.1    Nimmesgern, E.2    Wall, J.S.3    Hartl, F.-U.4    Horwich, A.L.5
  • 35
    • 0028196747 scopus 로고
    • Denaturants or cosolvents improve the specificity of PCR amplification of a G + C-rich DNA using genetically engineered DNA polymerases
    • DOI 10.1016/0378-1119(94)90723-4
    • Varadaraj K, Skinner DM. (1994). Denaturants or cosolvents improve the specificity of PCR amplification of a G + C-rich DNA using genetically engineered DNA polymerases. Gene 140: 1-5. (Pubitemid 24082369)
    • (1994) Gene , vol.140 , Issue.1 , pp. 1-5
    • Varadaraj, K.1    Skinner, D.M.2
  • 36
    • 74149088531 scopus 로고    scopus 로고
    • Resolution of phenotypically distinct strains of Enterococcus spp. in a complex microbial community using cpn60 universal target sequencing
    • Vermette CJ, Russell AH, Desai AR, Hill JE. (2010). Resolution of phenotypically distinct strains of Enterococcus spp. in a complex microbial community using cpn60 universal target sequencing. Microb Ecol 59: 14-24.
    • (2010) Microb Ecol , vol.59 , pp. 14-24
    • Vermette, C.J.1    Russell, A.H.2    Desai, A.R.3    Hill, J.E.4
  • 37
  • 38
    • 68149160400 scopus 로고    scopus 로고
    • Application of recA and rpoB sequence analysis on phylogeny and molecular identification of Geobacillus species
    • Weng FY, Chiou CS, Lin PH, Yang SS. (2009). Application of recA and rpoB sequence analysis on phylogeny and molecular identification of Geobacillus species. J Appl Microbiol 107: 452-464.
    • (2009) J Appl Microbiol , vol.107 , pp. 452-464
    • Weng, F.Y.1    Chiou, C.S.2    Lin, P.H.3    Yang, S.S.4
  • 41
    • 34447511716 scopus 로고    scopus 로고
    • Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada
    • DOI 10.1128/AEM.00103-07
    • Wright AD, Auckland CH, Lynn DH. (2007). Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada. Appl Environ Microbiol 73: 4206-4210. (Pubitemid 47068159)
    • (2007) Applied and Environmental Microbiology , vol.73 , Issue.13 , pp. 4206-4210
    • Wright, A.-D.G.1    Auckland, C.H.2    Lynn, D.H.3
  • 43
    • 0032835111 scopus 로고    scopus 로고
    • Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon
    • Yap WH, Zhang Z, Wang Y. (1999). Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J Bacteriol 181: 5201-5209. (Pubitemid 29416337)
    • (1999) Journal of Bacteriology , vol.181 , Issue.17 , pp. 5201-5209
    • Wai Ho, Y.1    Zhang, Z.2    Wang, Y.3
  • 44
    • 19644362750 scopus 로고    scopus 로고
    • Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus
    • DOI 10.1099/ijs.0.63452-0, 63452
    • Zeigler DR. (2005). Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus. Int J Syst Evol Microbiol 55: 1171-1179. (Pubitemid 40740188)
    • (2005) International Journal of Systematic and Evolutionary Microbiology , vol.55 , Issue.3 , pp. 1171-1179
    • Zeigler, D.R.1
  • 45
    • 70349908270 scopus 로고    scopus 로고
    • Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies
    • Zhou M, Hernandez-Sanabria E, Guan LL. (2009). Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. Appl Environ Microbiol 75: 6524-6533.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 6524-6533
    • Zhou, M.1    Hernandez-Sanabria, E.2    Guan, L.L.3


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