메뉴 건너뛰기




Volumn 41, Issue , 2014, Pages 253-274

Bacterial typing and identification by genomic analysis of 16S-23S rRNA intergenic transcribed spacer (ITS) sequences

Author keywords

16S rRNA; 23S rRNA intergenic transcribed spacer; App; Bacteria; FileMaker; Identification; RiboTyping; Typing

Indexed keywords


EID: 84919423273     PISSN: 05809517     EISSN: None     Source Type: Book Series    
DOI: 10.1016/bs.mim.2014.07.004     Document Type: Chapter
Times cited : (17)

References (36)
  • 1
    • 0028946084 scopus 로고
    • Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    • Amann R.I., Ludwig W., Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 1995, 59:143-169.
    • (1995) Microbiological Reviews , vol.59 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.H.3
  • 2
    • 29144504177 scopus 로고    scopus 로고
    • At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies
    • Ashelford K.E., Chuzhanova N.A., Fry J.C., Jones A.J., Weightman A.J. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Applied and Environmental Microbiology 2005, 71:7724-7736.
    • (2005) Applied and Environmental Microbiology , vol.71 , pp. 7724-7736
    • Ashelford, K.E.1    Chuzhanova, N.A.2    Fry, J.C.3    Jones, A.J.4    Weightman, A.J.5
  • 5
    • 0032954830 scopus 로고    scopus 로고
    • Analysis of 16S-23S rRNA intergenic spacer regions of Vibrio cholerae and Vibrio mimicus
    • Chun J., Huq A., Colwell R.R. Analysis of 16S-23S rRNA intergenic spacer regions of Vibrio cholerae and Vibrio mimicus. Applied and Environmental Microbiology 1999, 65:2202-2208.
    • (1999) Applied and Environmental Microbiology , vol.65 , pp. 2202-2208
    • Chun, J.1    Huq, A.2    Colwell, R.R.3
  • 6
    • 0242552653 scopus 로고    scopus 로고
    • Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes
    • Coenye T., Vandamme P. Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. FEMS Microbiology Letters 2003, 228:45-49.
    • (2003) FEMS Microbiology Letters , vol.228 , pp. 45-49
    • Coenye, T.1    Vandamme, P.2
  • 7
    • 58149200948 scopus 로고    scopus 로고
    • The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis
    • Cole J.R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., et al. The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Research 2009, 37:D141-D145.
    • (2009) Nucleic Acids Research , vol.37 , pp. D141-D145
    • Cole, J.R.1    Wang, Q.2    Cardenas, E.3    Fish, J.4    Chai, B.5    Farris, R.J.6
  • 9
    • 33644856111 scopus 로고    scopus 로고
    • IWoCS: Analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships
    • D'Auria G., Pushker R., Rodriguez-Valera F. IWoCS: Analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships. Bioinformatics 2006, 22:527-531.
    • (2006) Bioinformatics , vol.22 , pp. 527-531
    • D'Auria, G.1    Pushker, R.2    Rodriguez-Valera, F.3
  • 15
    • 33645074130 scopus 로고    scopus 로고
    • Variation in the 16S-23S rRNA intergenic spacer regions in Vibrio parahaemolyticus strains are due to indels nearby their tRNAGlu
    • Gonzalez-Escalona N., Romero J., Guzman C.A., Espejo R.T. Variation in the 16S-23S rRNA intergenic spacer regions in Vibrio parahaemolyticus strains are due to indels nearby their tRNAGlu. FEMS Microbiology Letters 2006, 256:38-43.
    • (2006) FEMS Microbiology Letters , vol.256 , pp. 38-43
    • Gonzalez-Escalona, N.1    Romero, J.2    Guzman, C.A.3    Espejo, R.T.4
  • 16
    • 0344172783 scopus 로고    scopus 로고
    • The role of recombination and mutation in 16S-23S rDNA spacer rearrangements
    • Gurtler V. The role of recombination and mutation in 16S-23S rDNA spacer rearrangements. Gene 1999, 238:241-252.
    • (1999) Gene , vol.238 , pp. 241-252
    • Gurtler, V.1
  • 17
    • 0029057279 scopus 로고
    • Typing of Staphylococcus aureus strains by PCR-amplification of variable-length 16S-23S rDNA spacer regions: Characterization of spacer sequences
    • Gurtler V., Barrie H.D. Typing of Staphylococcus aureus strains by PCR-amplification of variable-length 16S-23S rDNA spacer regions: Characterization of spacer sequences. Microbiology (Reading, England) 1995, 141(Pt. 5):1255-1265.
    • (1995) Microbiology (Reading, England) , vol.141 , pp. 1255-1265
    • Gurtler, V.1    Barrie, H.D.2
  • 18
    • 84877120397 scopus 로고    scopus 로고
    • New opportunities for improved ribotyping of C. difficile clinical isolates by exploring their genomes
    • Gurtler V., Grando D. New opportunities for improved ribotyping of C. difficile clinical isolates by exploring their genomes. Journal of Microbiological Methods 2013, 93:257-272.
    • (2013) Journal of Microbiological Methods , vol.93 , pp. 257-272
    • Gurtler, V.1    Grando, D.2
  • 19
    • 30944461986 scopus 로고    scopus 로고
    • Direct identification of slowly growing Mycobacterium species by analysis of the intergenic 16S-23S rDNA spacer region (ISR) using a GelCompar II database containing sequence based optimization for restriction fragment site polymorphisms (RFLPs) for 12 enzymes
    • Gurtler V., Harford C., Bywater J., Mayall B.C. Direct identification of slowly growing Mycobacterium species by analysis of the intergenic 16S-23S rDNA spacer region (ISR) using a GelCompar II database containing sequence based optimization for restriction fragment site polymorphisms (RFLPs) for 12 enzymes. Journal of Microbiological Methods 2006, 64:185-199.
    • (2006) Journal of Microbiological Methods , vol.64 , pp. 185-199
    • Gurtler, V.1    Harford, C.2    Bywater, J.3    Mayall, B.C.4
  • 20
    • 0030054296 scopus 로고    scopus 로고
    • New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region
    • Gurtler V., Stanisich V.A. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology (Reading, England) 1996, 142(Pt. 1):3-16.
    • (1996) Microbiology (Reading, England) , vol.142 , pp. 3-16
    • Gurtler, V.1    Stanisich, V.A.2
  • 21
    • 0026094568 scopus 로고
    • Classification of medically important clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA
    • Gurtler V., Wilson V.A., Mayall B.C. Classification of medically important clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA. Journal of General Microbiology 1991, 137:2673-2679.
    • (1991) Journal of General Microbiology , vol.137 , pp. 2673-2679
    • Gurtler, V.1    Wilson, V.A.2    Mayall, B.C.3
  • 23
    • 0036084147 scopus 로고    scopus 로고
    • RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database
    • Harmsen D., Rothganger J., Frosch M., Albert J. RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database. Nucleic Acids Research 2002, 30:416-417.
    • (2002) Nucleic Acids Research , vol.30 , pp. 416-417
    • Harmsen, D.1    Rothganger, J.2    Frosch, M.3    Albert, J.4
  • 25
    • 77957772756 scopus 로고    scopus 로고
    • The glycobiome of the rumen bacterium Butyrivibrio proteoclasticus B316(T) highlights adaptation to a polysaccharide-rich environment
    • Kelly W.J., Leahy S.C., Altermann E., Yeoman C.J., Dunne J.C., Kong Z., et al. The glycobiome of the rumen bacterium Butyrivibrio proteoclasticus B316(T) highlights adaptation to a polysaccharide-rich environment. PLoS One 2010, 5:e11942.
    • (2010) PLoS One , vol.5 , pp. e11942
    • Kelly, W.J.1    Leahy, S.C.2    Altermann, E.3    Yeoman, C.J.4    Dunne, J.C.5    Kong, Z.6
  • 26
    • 58149179980 scopus 로고    scopus 로고
    • RrnDB: Documenting the number of rRNA and tRNA genes in bacteria and archaea
    • Lee Z.M., Bussema C., Schmidt T.M. rrnDB: Documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Research 2009, 37:D489-D493.
    • (2009) Nucleic Acids Research , vol.37 , pp. D489-D493
    • Lee, Z.M.1    Bussema, C.2    Schmidt, T.M.3
  • 27
    • 84912024870 scopus 로고    scopus 로고
    • Atypical bacterial rRNA operon structure is prevalent within the Lachnospiraceae, and use of the 16S-23S rRNA internal transcribed spacer region for the rapid identification of ruminal Butyrivibrio and Pseudobutyrivibrio strains
    • Li D., Leahy S., Henderson G., Kelly W., Cookson A., Attwood G., et al. Atypical bacterial rRNA operon structure is prevalent within the Lachnospiraceae, and use of the 16S-23S rRNA internal transcribed spacer region for the rapid identification of ruminal Butyrivibrio and Pseudobutyrivibrio strains. Annals of Microbiology 2014, 10.1007/s13213-014-0806-2.
    • (2014) Annals of Microbiology
    • Li, D.1    Leahy, S.2    Henderson, G.3    Kelly, W.4    Cookson, A.5    Attwood, G.6
  • 29
    • 23744479443 scopus 로고    scopus 로고
    • Computational approach involving use of the internal transcribed spacer 1 region for identification of Mycobacterium species
    • Mohamed A.M., Kuyper D.J., Iwen P.C., Ali H.H., Bastola D.R., Hinrichs S.H. Computational approach involving use of the internal transcribed spacer 1 region for identification of Mycobacterium species. Journal of Clinical Microbiology 2005, 43:3811-3817.
    • (2005) Journal of Clinical Microbiology , vol.43 , pp. 3811-3817
    • Mohamed, A.M.1    Kuyper, D.J.2    Iwen, P.C.3    Ali, H.H.4    Bastola, D.R.5    Hinrichs, S.H.6
  • 30
    • 15144358617 scopus 로고    scopus 로고
    • Variation of the ribosomal operon 16S-23S gene spacer region in representatives of Salmonella enterica subspecies
    • Perez Luz S., Rodriguez-Valera F., Lan R., Reeves P.R. Variation of the ribosomal operon 16S-23S gene spacer region in representatives of Salmonella enterica subspecies. Journal of Bacteriology 1998, 180:2144-2151.
    • (1998) Journal of Bacteriology , vol.180 , pp. 2144-2151
    • Perez Luz, S.1    Rodriguez-Valera, F.2    Lan, R.3    Reeves, P.R.4
  • 31
    • 37549027613 scopus 로고    scopus 로고
    • SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • Pruesse E., Quast C., Knittel K., Fuchs B.M., Ludwig W., Peplies J., et al. SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research 2007, 35:7188-7196.
    • (2007) Nucleic Acids Research , vol.35 , pp. 7188-7196
    • Pruesse, E.1    Quast, C.2    Knittel, K.3    Fuchs, B.M.4    Ludwig, W.5    Peplies, J.6
  • 32
    • 33750972041 scopus 로고    scopus 로고
    • The mosaic nature of intergenic 16S-23S rRNA spacer regions suggests rRNA operon copy number variation in Clostridium difficile strains
    • Sadeghifard N., Gurtler V., Beer M., Seviour R.J. The mosaic nature of intergenic 16S-23S rRNA spacer regions suggests rRNA operon copy number variation in Clostridium difficile strains. Applied and Environmental Microbiology 2006, 72:7311-7323.
    • (2006) Applied and Environmental Microbiology , vol.72 , pp. 7311-7323
    • Sadeghifard, N.1    Gurtler, V.2    Beer, M.3    Seviour, R.J.4
  • 33
    • 84892486136 scopus 로고    scopus 로고
    • Evaluation of 16SpathDB 2.0, an automated 16S rRNA gene sequence database, using 689 complete bacterial genomes
    • Teng J.L., Ho T.C., Yeung R.S., Wong A.Y., Wang H., Chen C., et al. Evaluation of 16SpathDB 2.0, an automated 16S rRNA gene sequence database, using 689 complete bacterial genomes. Diagnostic Microbiology and Infectious Disease 2014, 78:105-115.
    • (2014) Diagnostic Microbiology and Infectious Disease , vol.78 , pp. 105-115
    • Teng, J.L.1    Ho, T.C.2    Yeung, R.S.3    Wong, A.Y.4    Wang, H.5    Chen, C.6
  • 36
    • 84893976081 scopus 로고    scopus 로고
    • A simple one-step PCR walking method and its application of bacterial rRNA for sequencing identification
    • Zhang H., You C., Ren J., Xu D., Han M., Liao W. A simple one-step PCR walking method and its application of bacterial rRNA for sequencing identification. Current Microbiology 2014, 68:486-494.
    • (2014) Current Microbiology , vol.68 , pp. 486-494
    • Zhang, H.1    You, C.2    Ren, J.3    Xu, D.4    Han, M.5    Liao, W.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.