메뉴 건너뛰기




Volumn 8, Issue 7, 2013, Pages

Comparison of DNA Extraction Methods in Analysis of Salivary Bacterial Communities

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S;

EID: 84879755675     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0067699     Document Type: Article
Times cited : (69)

References (39)
  • 1
    • 79952201936 scopus 로고    scopus 로고
    • Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health
    • Crielaard W, Zaura E, Schuller AA, Huse SM, Montijn RC, et al. (2011) Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health. BMC Med Genomics 4: 22.
    • (2011) BMC Med Genomics , vol.4 , pp. 22
    • Crielaard, W.1    Zaura, E.2    Schuller, A.A.3    Huse, S.M.4    Montijn, R.C.5
  • 3
    • 27344434131 scopus 로고    scopus 로고
    • The salivary microbiota as a diagnostic indicator of oral cancer: a descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects
    • Mager DL, Haffajee AD, Devlin PM, Norris CM, Posner MR, et al. (2005) The salivary microbiota as a diagnostic indicator of oral cancer: a descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects. J Transl Med 3: 27.
    • (2005) J Transl Med , vol.3 , pp. 27
    • Mager, D.L.1    Haffajee, A.D.2    Devlin, P.M.3    Norris, C.M.4    Posner, M.R.5
  • 5
    • 0038260204 scopus 로고
    • A bacteriologic census of human saliva
    • Richardson RL, Jones M, (1958) A bacteriologic census of human saliva. J Dent Res 37: 697-709.
    • (1958) J Dent Res , vol.37 , pp. 697-709
    • Richardson, R.L.1    Jones, M.2
  • 6
    • 0015156689 scopus 로고
    • Quantitative studies on the salivary flora
    • Ross PW, (1971) Quantitative studies on the salivary flora. Journal of clinical pathology 24: 717-720.
    • (1971) Journal of Clinical Pathology , vol.24 , pp. 717-720
    • Ross, P.W.1
  • 7
    • 82555183004 scopus 로고    scopus 로고
    • The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information
    • Chen T, Yu WH, Izard J, Baranova OV, Lakshmanan A, et al. (2010) The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford) 2010: baq013.
    • (2010) Database (Oxford) , vol.2010
    • Chen, T.1    Yu, W.H.2    Izard, J.3    Baranova, O.V.4    Lakshmanan, A.5
  • 9
    • 80051514697 scopus 로고    scopus 로고
    • Comparative analysis of salivary bacterial microbiome diversity in edentulous infants and their mothers or primary care givers using pyrosequencing
    • Cephas KD, Kim J, Mathai RA, Barry KA, Dowd SE, et al. (2011) Comparative analysis of salivary bacterial microbiome diversity in edentulous infants and their mothers or primary care givers using pyrosequencing. PLoS ONE 6: e23503.
    • (2011) PLoS ONE , vol.6
    • Cephas, K.D.1    Kim, J.2    Mathai, R.A.3    Barry, K.A.4    Dowd, S.E.5
  • 12
    • 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
  • 15
    • 69949120119 scopus 로고    scopus 로고
    • Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray
    • Colombo AP, Boches SK, Cotton SL, Goodson JM, Kent R, et al. (2009) Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray. J Periodontol 80: 1421-1432.
    • (2009) J Periodontol , vol.80 , pp. 1421-1432
    • Colombo, A.P.1    Boches, S.K.2    Cotton, S.L.3    Goodson, J.M.4    Kent, R.5
  • 16
    • 39149112256 scopus 로고    scopus 로고
    • Microbiological diversity of generalized aggressive periodontitis by 16S rRNA clonal analysis
    • Faveri M, Mayer MP, Feres M, de Figueiredo LC, Dewhirst FE, et al. (2008) Microbiological diversity of generalized aggressive periodontitis by 16S rRNA clonal analysis. Oral Microbiol Immunol 23: 112-118.
    • (2008) Oral Microbiol Immunol , vol.23 , pp. 112-118
    • Faveri, M.1    Mayer, M.P.2    Feres, M.3    de Figueiredo, L.C.4    Dewhirst, F.E.5
  • 17
    • 70350125099 scopus 로고    scopus 로고
    • Human gut microbiome adopts an alternative state following small bowel transplantation
    • Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, et al. (2009) Human gut microbiome adopts an alternative state following small bowel transplantation. Proc Natl Acad Sci U S A 106: 17187-17192.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 17187-17192
    • Hartman, A.L.1    Lough, D.M.2    Barupal, D.K.3    Fiehn, O.4    Fishbein, T.5
  • 18
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
    • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 7537-7541
    • Schloss, P.D.1    Westcott, S.L.2    Ryabin, T.3    Hall, J.R.4    Hartmann, M.5
  • 19
    • 84857122937 scopus 로고    scopus 로고
    • An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    • McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, et al. (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. The ISME journal 6: 610-618.
    • (2012) The ISME Journal , vol.6 , pp. 610-618
    • McDonald, D.1    Price, M.N.2    Goodrich, J.3    Nawrocki, E.P.4    DeSantis, T.Z.5
  • 20
    • 77955251092 scopus 로고    scopus 로고
    • Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    • Huse SM, Welch DM, Morrison HG, Sogin ML, (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environmental microbiology 12: 1889-1898.
    • (2010) Environmental Microbiology , vol.12 , pp. 1889-1898
    • Huse, S.M.1    Welch, D.M.2    Morrison, H.G.3    Sogin, M.L.4
  • 22
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 23
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximum-likelihood trees for large alignments
    • Price MN, Dehal PS, Arkin AP, (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5: e9490.
    • (2010) PLoS ONE , vol.5
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 24
    • 73449128271 scopus 로고    scopus 로고
    • Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
    • Hamady M, Lozupone C, Knight R, (2010) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4: 17-27.
    • (2010) ISME J , vol.4 , pp. 17-27
    • Hamady, M.1    Lozupone, C.2    Knight, R.3
  • 25
    • 79952006773 scopus 로고    scopus 로고
    • Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
    • Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, et al. (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research 21: 494-504.
    • (2011) Genome Research , vol.21 , pp. 494-504
    • Haas, B.J.1    Gevers, D.2    Earl, A.M.3    Feldgarden, M.4    Ward, D.V.5
  • 27
    • 77949601825 scopus 로고    scopus 로고
    • CD-HIT Suite: a web server for clustering and comparing biological sequences
    • Huang Y, Niu B, Gao Y, Fu L, Li W, (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26: 680-682.
    • (2010) Bioinformatics , vol.26 , pp. 680-682
    • Huang, Y.1    Niu, B.2    Gao, Y.3    Fu, L.4    Li, W.5
  • 28
    • 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, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-145.
    • (2009) Nucleic Acids Res , vol.37
    • Cole, J.R.1    Wang, Q.2    Cardenas, E.3    Fish, J.4    Chai, B.5
  • 29
    • 0000286531 scopus 로고
    • An ordination of the upland forest communities of southern Wisconsin
    • Bray R, Curtis JT, (1957) An ordination of the upland forest communities of southern Wisconsin. Ecological Monographs 27: 325-334.
    • (1957) Ecological Monographs , vol.27 , pp. 325-334
    • Bray, R.1    Curtis, J.T.2
  • 30
    • 0031284508 scopus 로고    scopus 로고
    • Species assemblages and indicator species: The need for a flexible asymmetrical approach
    • Dufrêne M, Legendre P, (1997) Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecological Monographs 67: 345-366.
    • (1997) Ecological Monographs , vol.67 , pp. 345-366
    • Dufrêne, M.1    Legendre, P.2
  • 32
  • 33
    • 84861546470 scopus 로고    scopus 로고
    • High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature
    • Sergeant MJ, Constantinidou C, Cogan T, Penn CW, Pallen MJ, (2012) High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature. PLoS ONE 7: e38094.
    • (2012) PLoS ONE , vol.7
    • Sergeant, M.J.1    Constantinidou, C.2    Cogan, T.3    Penn, C.W.4    Pallen, M.J.5
  • 34
    • 78751575501 scopus 로고    scopus 로고
    • UniFrac: an effective distance metric for microbial community comparison
    • Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R, (2011) UniFrac: an effective distance metric for microbial community comparison. ISME J 5: 169-172.
    • (2011) ISME J , vol.5 , pp. 169-172
    • Lozupone, C.1    Lladser, M.E.2    Knights, D.3    Stombaugh, J.4    Knight, R.5
  • 36
    • 84863292680 scopus 로고    scopus 로고
    • Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection
    • Biesbroek G, Sanders EA, Roeselers G, Wang X, Caspers MP, et al. (2012) Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection. PLoS ONE 7: e32942.
    • (2012) PLoS ONE , vol.7
    • Biesbroek, G.1    Sanders, E.A.2    Roeselers, G.3    Wang, X.4    Caspers, M.P.5
  • 37
    • 84862072074 scopus 로고    scopus 로고
    • Simplified protocols for the preparation of genomic DNA from bacterial cultures
    • In: Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans ADL, van Elsas JD, editors. Dordrecht: Kluwer Academic Publishers
    • Moore ERB, Arnscheidt A, Krüger A, Strömpl C, Mau M (2004) Simplified protocols for the preparation of genomic DNA from bacterial cultures. In: Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans ADL, van Elsas JD, editors. Molecular Microbial Ecology Manual. Dordrecht: Kluwer Academic Publishers. 3-18.
    • (2004) Molecular Microbial Ecology Manual , pp. 3-18
    • Moore, E.R.B.1    Arnscheidt, A.2    Krüger, A.3    Strömpl, C.4    Mau, M.5
  • 38
    • 84859726078 scopus 로고    scopus 로고
    • Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples
    • Willner D, Daly J, Whiley D, Grimwood K, Wainwright CE, et al. (2012) Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples. PLoS ONE 7: e34605.
    • (2012) PLoS ONE , vol.7
    • Willner, D.1    Daly, J.2    Whiley, D.3    Grimwood, K.4    Wainwright, C.E.5
  • 39
    • 84858763397 scopus 로고    scopus 로고
    • Evaluation of methods for the extraction and purification of DNA from the human microbiome
    • Yuan S, Cohen DB, Ravel J, Abdo Z, Forney LJ, (2012) Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS ONE 7: e33865.
    • (2012) PLoS ONE , vol.7
    • Yuan, S.1    Cohen, D.B.2    Ravel, J.3    Abdo, Z.4    Forney, L.J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.