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Volumn 6, Issue 6, 2011, Pages

Target region selection is a critical determinant of community fingerprints generated by 16S Pyrosequencing

Author keywords

[No Author keywords available]

Indexed keywords

PRIMER RNA; RNA 16S;

EID: 79959677258     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020956     Document Type: Article
Times cited : (209)

References (40)
  • 1
    • 33646086251 scopus 로고    scopus 로고
    • Molecular characterization of subject-specific oral microflora during initial colonization of enamel
    • Diaz PI, Chalmers NI, Rickard AH, Kong C, Milburn CL, et al. (2006) Molecular characterization of subject-specific oral microflora during initial colonization of enamel. Appl Environ Microbiol 72: 2837-2848.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 2837-2848
    • Diaz, P.I.1    Chalmers, N.I.2    Rickard, A.H.3    Kong, C.4    Milburn, C.L.5
  • 2
    • 33645085330 scopus 로고    scopus 로고
    • Novel subgingival bacterial phylotypes detected using multiple universal polymerase chain reaction primer sets
    • de Lillo A, Ashley FP, Palmer RM, Munson MA, Kyriacou L, et al. (2006) Novel subgingival bacterial phylotypes detected using multiple universal polymerase chain reaction primer sets. Oral Microbiol Immunol 21: 61-68.
    • (2006) Oral Microbiol Immunol , vol.21 , pp. 61-68
    • de Lillo, A.1    Ashley, F.P.2    Palmer, R.M.3    Munson, M.A.4    Kyriacou, L.5
  • 4
    • 33750115389 scopus 로고    scopus 로고
    • Periodontal status in smokers and never-smokers: clinical findings and real-time polymerase chain reaction quantification of putative periodontal pathogens
    • Gomes SC, Piccinin FB, Oppermann RV, Susin C, Nonnenmacher CI, et al. (2006) Periodontal status in smokers and never-smokers: clinical findings and real-time polymerase chain reaction quantification of putative periodontal pathogens. J Periodontol 77: 1483-1490.
    • (2006) J Periodontol , vol.77 , pp. 1483-1490
    • Gomes, S.C.1    Piccinin, F.B.2    Oppermann, R.V.3    Susin, C.4    Nonnenmacher, C.I.5
  • 6
    • 0037258924 scopus 로고    scopus 로고
    • Molecular analysis of bacteria in periodontitis: evaluation of clone libraries, novel phylotypes and putative pathogens
    • Hutter G, Schlagenhauf U, Valenza G, Horn M, Burgemeister S, et al. (2003) Molecular analysis of bacteria in periodontitis: evaluation of clone libraries, novel phylotypes and putative pathogens. Microbiology 149: 67-75.
    • (2003) Microbiology , vol.149 , pp. 67-75
    • Hutter, G.1    Schlagenhauf, U.2    Valenza, G.3    Horn, M.4    Burgemeister, S.5
  • 7
    • 0033456272 scopus 로고    scopus 로고
    • Bacterial diversity within the human subgingival crevice
    • Kroes I, Lepp PW, Relman DA, (1999) Bacterial diversity within the human subgingival crevice. Proc Natl Acad Sci U S A 96: 14547-14552.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , pp. 14547-14552
    • Kroes, I.1    Lepp, P.W.2    Relman, D.A.3
  • 8
    • 23744438967 scopus 로고    scopus 로고
    • Identification of candidate periodontal pathogens and beneficial species by quantitative 16S clonal analysis
    • Kumar PS, Griffen AL, Moeschberger ML, Leys EJ, (2005) Identification of candidate periodontal pathogens and beneficial species by quantitative 16S clonal analysis. J Clin Microbiol 43: 3944-3955.
    • (2005) J Clin Microbiol , vol.43 , pp. 3944-3955
    • Kumar, P.S.1    Griffen, A.L.2    Moeschberger, M.L.3    Leys, E.J.4
  • 10
    • 73349110099 scopus 로고    scopus 로고
    • Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
    • Kunin V, Engelbrektson A, Ochman H, Hugenholtz P., Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123.
    • Environ Microbiol , vol.12 , pp. 118-123
    • Kunin, V.1    Engelbrektson, A.2    Ochman, H.3    Hugenholtz, P.4
  • 11
    • 74949134895 scopus 로고    scopus 로고
    • Defining the healthy "core microbiome" of oral microbial communities
    • Zaura E, Keijser BJ, Huse SM, Crielaard W, (2009) Defining the healthy "core microbiome" of oral microbial communities. BMC Microbiol 9: 259.
    • (2009) BMC Microbiol , vol.9 , pp. 259
    • Zaura, E.1    Keijser, B.J.2    Huse, S.M.3    Crielaard, W.4
  • 14
    • 77955386857 scopus 로고    scopus 로고
    • Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns
    • Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 107: 11971-11975.
    • Proc Natl Acad Sci U S A , vol.107 , pp. 11971-11975
    • Dominguez-Bello, M.G.1    Costello, E.K.2    Contreras, M.3    Magris, M.4    Hidalgo, G.5
  • 15
    • 0242384034 scopus 로고    scopus 로고
    • Review and re-analysis of domain-specific 16S primers
    • Baker GC, Smith JJ, Cowan DA, (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55: 541-555.
    • (2003) J Microbiol Methods , vol.55 , pp. 541-555
    • Baker, G.C.1    Smith, J.J.2    Cowan, D.A.3
  • 16
    • 70350527180 scopus 로고    scopus 로고
    • Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies
    • Wang Y, Qian PY, (2009) Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PLoS One 4: e7401.
    • (2009) PLoS One , vol.4
    • Wang, Y.1    Qian, P.Y.2
  • 17
    • 34147182303 scopus 로고    scopus 로고
    • A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria
    • Chakravorty S, Helb D, Burday M, Connell N, Alland D, (2007) A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 69: 330-339.
    • (2007) J Microbiol Methods , vol.69 , pp. 330-339
    • Chakravorty, S.1    Helb, D.2    Burday, M.3    Connell, N.4    Alland, D.5
  • 19
    • 68549130740 scopus 로고    scopus 로고
    • Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys
    • Youssef N, Sheik CS, Krumholz LR, Najar FZ, Roe BA, et al. (2009) Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl Environ Microbiol 75: 5227-5236.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 5227-5236
    • Youssef, N.1    Sheik, C.S.2    Krumholz, L.R.3    Najar, F.Z.4    Roe, B.A.5
  • 20
    • 78650453707 scopus 로고    scopus 로고
    • Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions
    • Claesson MJ, Wang Q, O'Sullivan O, Greene-Diniz R, Cole JR, et al. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res 38: e200.
    • Nucleic Acids Res , vol.38
    • Claesson, M.J.1    Wang, Q.2    O'Sullivan, O.3    Greene-Diniz, R.4    Cole, J.R.5
  • 21
    • 40749117643 scopus 로고    scopus 로고
    • Molecular identification of bacteria on the tongue dorsum of subjects with and without halitosis
    • Riggio MP, Lennon A, Rolph HJ, Hodge PJ, Donaldson A, et al. (2008) Molecular identification of bacteria on the tongue dorsum of subjects with and without halitosis. Oral Dis 14: 251-258.
    • (2008) Oral Dis , vol.14 , pp. 251-258
    • Riggio, M.P.1    Lennon, A.2    Rolph, H.J.3    Hodge, P.J.4    Donaldson, A.5
  • 22
    • 49949095159 scopus 로고    scopus 로고
    • Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs
    • Dowd SE, Sun Y, Wolcott RD, Domingo A, Carroll JA, (2008) Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog Dis 5: 459-472.
    • (2008) Foodborne Pathog Dis , vol.5 , pp. 459-472
    • Dowd, S.E.1    Sun, Y.2    Wolcott, R.D.3    Domingo, A.4    Carroll, J.A.5
  • 24
    • 33746061683 scopus 로고    scopus 로고
    • Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    • DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 5069-5072
    • DeSantis, T.Z.1    Hugenholtz, P.2    Larsen, N.3    Rojas, M.4    Brodie, E.L.5
  • 25
    • 67649327176 scopus 로고    scopus 로고
    • FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
    • %R 1610.1093/molbev/msp1077
    • Price MN, Dehal PS, Arkin AP, (2009) FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix. Molecular Biology and Evolution 26: 1641-1650 %R 1610.1093/molbev/msp1077.
    • (2009) Molecular Biology and Evolution , vol.26 , pp. 1641-1650
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 29
    • 5644227319 scopus 로고    scopus 로고
    • Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases
    • table of contents
    • Clarridge JE 3rd, (2004) Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 17: 840-862 table of contents.
    • (2004) Clin Microbiol Rev , vol.17 , pp. 840-862
    • Clarridge 3rd., J.E.1
  • 30
    • 0035113093 scopus 로고    scopus 로고
    • Rapid ribosequencing-an effective diagnostic tool for detecting microbial infection
    • Trotha R, Hanck T, Konig W, Konig B, (2001) Rapid ribosequencing-an effective diagnostic tool for detecting microbial infection. Infection 29: 12-16.
    • (2001) Infection , vol.29 , pp. 12-16
    • Trotha, R.1    Hanck, T.2    Konig, W.3    Konig, B.4
  • 31
    • 0031178951 scopus 로고    scopus 로고
    • The mathematical theory of communication. 1963
    • Shannon CE, (1997) The mathematical theory of communication. 1963. MD Comput 14: 306-317.
    • (1997) MD Comput , vol.14 , pp. 306-317
    • Shannon, C.E.1
  • 33
    • 34248635940 scopus 로고    scopus 로고
    • Changes in periodontal health status are associated with bacterial community shifts as assessed by quantitative 16S cloning and sequencing
    • Kumar PS, Leys EJ, Bryk JM, Martinez FJ, Moeschberger ML, et al. (2006) Changes in periodontal health status are associated with bacterial community shifts as assessed by quantitative 16S cloning and sequencing. J Clin Microbiol 44: 3665-3673.
    • (2006) J Clin Microbiol , vol.44 , pp. 3665-3673
    • Kumar, P.S.1    Leys, E.J.2    Bryk, J.M.3    Martinez, F.J.4    Moeschberger, M.L.5
  • 34
    • 65349091290 scopus 로고    scopus 로고
    • Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure
    • Huber JA, Morrison HG, Huse SM, Neal PR, Sogin ML, et al. (2009) Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environ Microbiol 11: 1292-1302.
    • (2009) Environ Microbiol , vol.11 , pp. 1292-1302
    • Huber, J.A.1    Morrison, H.G.2    Huse, S.M.3    Neal, P.R.4    Sogin, M.L.5
  • 35
    • 0031711754 scopus 로고    scopus 로고
    • Bias in template-to-product ratios in multitemplate PCR
    • Polz MF, Cavanaugh CM, (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64: 3724-3730.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 3724-3730
    • Polz, M.F.1    Cavanaugh, C.M.2
  • 36
    • 0031796891 scopus 로고    scopus 로고
    • Novel short-fragment PCR assay for highly sensitive broad-spectrum detection of anogenital human papillomaviruses
    • Kleter B, van Doorn LJ, ter Schegget J, Schrauwen L, van Krimpen K, et al. (1998) Novel short-fragment PCR assay for highly sensitive broad-spectrum detection of anogenital human papillomaviruses. Am J Pathol 153: 1731-1739.
    • (1998) Am J Pathol , vol.153 , pp. 1731-1739
    • Kleter, B.1    van Doorn, L.J.2    ter Schegget, J.3    Schrauwen, L.4    van Krimpen, K.5
  • 37
    • 0030067991 scopus 로고    scopus 로고
    • Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
    • Suzuki MT, Giovannoni SJ, (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62: 625-630.
    • (1996) Appl Environ Microbiol , vol.62 , pp. 625-630
    • Suzuki, M.T.1    Giovannoni, S.J.2
  • 38
    • 0035410959 scopus 로고    scopus 로고
    • Sequence microdiversity at the ribosomal RNA operons of Escherichia coli pyelonephritogenic strains
    • Anton AI, Martinez-Murcia AJ, Rodriguez-Valera F, Dalet F, (2001) Sequence microdiversity at the ribosomal RNA operons of Escherichia coli pyelonephritogenic strains. Clin Microbiol Infect 7: 345-351.
    • (2001) Clin Microbiol Infect , vol.7 , pp. 345-351
    • Anton, A.I.1    Martinez-Murcia, A.J.2    Rodriguez-Valera, F.3    Dalet, F.4
  • 39
    • 0344780794 scopus 로고    scopus 로고
    • Patterns of sequence variation in two regions of the 16S rRNA multigene family of Escherichia coli
    • Martinez-Murcia AJ, Anton AI, Rodriguez-Valera F, (1999) Patterns of sequence variation in two regions of the 16S rRNA multigene family of Escherichia coli. Int J Syst Bacteriol 49 Pt 2: 601-610.
    • (1999) Int J Syst Bacteriol , vol.49 , Issue.Pt 2 , pp. 601-610
    • Martinez-Murcia, A.J.1    Anton, A.I.2    Rodriguez-Valera, F.3
  • 40
    • 0031790538 scopus 로고    scopus 로고
    • Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity
    • Suzuki M, Rappe MS, Giovannoni SJ, (1998) Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl Environ Microbiol 64: 4522-4529.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 4522-4529
    • Suzuki, M.1    Rappe, M.S.2    Giovannoni, S.J.3


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