메뉴 건너뛰기




Volumn 25, Issue 6, 2010, Pages 391-405

Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing

Author keywords

Dental plaque; Fragment recruitment; Human oral microbiome; Metagenomic sequencing; Next generation sequencing; Oralgen

Indexed keywords

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; GENE SEQUENCE; GENOME; HUMAN; METAGENOMICS; MICROFLORA; MOUTH DISEASE; PATHOGENESIS; TOOTH FLORA; TOOTH PLAQUE;

EID: 78049415520     PISSN: 20411006     EISSN: 20411014     Source Type: Journal    
DOI: 10.1111/j.2041-1014.2010.00587.x     Document Type: Article
Times cited : (76)

References (38)
  • 2
    • 42449131386 scopus 로고    scopus 로고
    • Bacteria of dental caries in primary and permanent teeth in children and young adults
    • Aas, J.A., Griffen, A.L., Dardis, S.R. et al. (2008) Bacteria of dental caries in primary and permanent teeth in children and young adults. J Clin Microbiol 46: 1407-1417.
    • (2008) J Clin Microbiol , vol.46 , pp. 1407-1417
    • Aas, J.A.1    Griffen, A.L.2    Dardis, S.R.3
  • 4
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul, S.F., Madden, T.L., Schaffer, A.A. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3
  • 5
    • 40549120596 scopus 로고    scopus 로고
    • The RAST server: rapid annotations using subsystems technology
    • Aziz, R.K., Bartels, D., Best, A.A. et al. (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
    • (2008) BMC Genomics , vol.9 , pp. 75
    • Aziz, R.K.1    Bartels, D.2    Best, A.A.3
  • 6
    • 0036197764 scopus 로고    scopus 로고
    • Molecular analysis of bacterial species associated with childhood caries
    • Becker, M.R., Paster, B.J., Leys, E.J. et al. (2002) Molecular analysis of bacterial species associated with childhood caries. J Clin Microbiol 40: 1001-1009.
    • (2002) J Clin Microbiol , vol.40 , pp. 1001-1009
    • Becker, M.R.1    Paster, B.J.2    Leys, E.J.3
  • 7
    • 0035751189 scopus 로고    scopus 로고
    • Bioinformatics issues for automating the annotation of genomic sequences
    • Carter, K., Oka, A., Tamiya, G. and Bellgard, M.I. (2001) Bioinformatics issues for automating the annotation of genomic sequences. Genome Inform 12: 204-211.
    • (2001) Genome Inform , vol.12 , pp. 204-211
    • Carter, K.1    Oka, A.2    Tamiya, G.3    Bellgard, M.I.4
  • 8
    • 0036137277 scopus 로고    scopus 로고
    • DNA sequence quality trimming and vector removal
    • Chou, H.H. and Holmes, M.H. (2001) DNA sequence quality trimming and vector removal. Bioinformatics 17: 1093-1104.
    • (2001) Bioinformatics , vol.17 , pp. 1093-1104
    • Chou, H.H.1    Holmes, M.H.2
  • 9
    • 33744804299 scopus 로고    scopus 로고
    • Metagenomic analysis of the human distal gut microbiome
    • Gill, S.R., Pop, M., Deboy, R.T. et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359.
    • (2006) Science , vol.312 , pp. 1355-1359
    • Gill, S.R.1    Pop, M.2    Deboy, R.T.3
  • 10
    • 20444447524 scopus 로고    scopus 로고
    • Microbiology of periodontal diseases: introduction
    • Haffajee, A.D. and Socransky, S.S. (2005) Microbiology of periodontal diseases: introduction. Periodontol 2000 38: 9-12.
    • (2005) Periodontol 2000 , vol.38 , pp. 9-12
    • Haffajee, A.D.1    Socransky, S.S.2
  • 11
    • 33747827173 scopus 로고    scopus 로고
    • Introduction to microbial aspects of periodontal biofilm communities, development and treatment
    • Haffajee, A.D. and Socransky, S.S. (2006) Introduction to microbial aspects of periodontal biofilm communities, development and treatment. Periodontol 2000 42: 7-12.
    • (2006) Periodontol 2000 , vol.42 , pp. 7-12
    • Haffajee, A.D.1    Socransky, S.S.2
  • 13
    • 58149218590 scopus 로고    scopus 로고
    • Pyrosequencing analysis of the oral microflora of healthy adults
    • Keijser, B.J., Zaura, E., Huse, S.M. et al. (2008) Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res 87: 1016-1020.
    • (2008) J Dent Res , vol.87 , pp. 1016-1020
    • Keijser, B.J.1    Zaura, E.2    Huse, S.M.3
  • 14
    • 0033456272 scopus 로고    scopus 로고
    • Bacterial diversity within the human subgingival crevice
    • Kroes, I., Lepp, P.W. and Relman, D.A. (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
  • 16
    • 2942538300 scopus 로고    scopus 로고
    • Versatile and open software for comparing large genomes
    • Kurtz, S., Phillippy, A., Delcher, A.L. et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.
    • (2004) Genome Biol , vol.5
    • Kurtz, S.1    Phillippy, A.2    Delcher, A.L.3
  • 17
    • 70449530747 scopus 로고    scopus 로고
    • Metagenomic study of the oral microbiota by Illumina high-throughput sequencing
    • Lazarevic, V., Whiteson, K., Huse, S. et al. (2009) Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Meth 79: 266-271.
    • (2009) J Microbiol Meth , vol.79 , pp. 266-271
    • Lazarevic, V.1    Whiteson, K.2    Huse, S.3
  • 18
    • 38549139537 scopus 로고    scopus 로고
    • IMG/M: a data management and analysis system for metagenomes
    • other authors
    • Markowitz, V.M., Ivanova, N.N. and Szeto, E. and other authors (2008) IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res 36: D534-D538.
    • (2008) Nucleic Acids Res , vol.36
    • Markowitz, V.M.1    Ivanova, N.N.2    Szeto, E.3
  • 19
    • 0028475512 scopus 로고
    • Microbial ecology of dental plaque and its significance in health and disease
    • Marsh, P.D. (1994) Microbial ecology of dental plaque and its significance in health and disease. Adv Dent Res 8: 263-271.
    • (1994) Adv Dent Res , vol.8 , pp. 263-271
    • Marsh, P.D.1
  • 20
    • 39049181743 scopus 로고    scopus 로고
    • Dental diseases - are these examples of ecological catastrophes?
    • discussion 50-52.
    • Marsh, P.D. (2006) Dental diseases - are these examples of ecological catastrophes? Int J Dent Hyg 4(Suppl 1): 3-10; discussion 50-52.
    • (2006) Int J Dent Hyg , vol.4 , Issue.SUPPL 1 , pp. 3-10
    • Marsh, P.D.1
  • 21
    • 63849171250 scopus 로고    scopus 로고
    • Global diversity in the human salivary microbiome
    • Nasidze, I., Li, J., Quinque, D., Tang, K. and Stoneking, M. (2009) Global diversity in the human salivary microbiome. Genome Res 19: 636-643.
    • (2009) Genome Res , vol.19 , pp. 636-643
    • Nasidze, I.1    Li, J.2    Quinque, D.3    Tang, K.4    Stoneking, M.5
  • 22
    • 33750976398 scopus 로고    scopus 로고
    • MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
    • Noguchi, H., Park, J. and Takagi, T. (2006) MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res 34: 5623-5630.
    • (2006) Nucleic Acids Res , vol.34 , pp. 5623-5630
    • Noguchi, H.1    Park, J.2    Takagi, T.3
  • 23
    • 25644458211 scopus 로고    scopus 로고
    • The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    • Overbeek, R., Begley, T., Butler, R.M. et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33: 5691-5702.
    • (2005) Nucleic Acids Res , vol.33 , pp. 5691-5702
    • Overbeek, R.1    Begley, T.2    Butler, R.M.3
  • 24
    • 0034992657 scopus 로고    scopus 로고
    • Bacterial diversity in human subgingival plaque
    • Paster, B.J., Boches, S.K., Galvin, J.L. et al. (2001) Bacterial diversity in human subgingival plaque. J Bacteriol 183: 3770-3783.
    • (2001) J Bacteriol , vol.183 , pp. 3770-3783
    • Paster, B.J.1    Boches, S.K.2    Galvin, J.L.3
  • 25
    • 33747853795 scopus 로고    scopus 로고
    • The breadth of bacterial diversity in the human periodontal pocket and other oral sites
    • Paster, B.J., Olsen, I., Aas, J.A. and Dewhirst, F.E. (2006) The breadth of bacterial diversity in the human periodontal pocket and other oral sites. Periodontol 2000 42: 80-87.
    • (2006) Periodontol 2000 , vol.42 , pp. 80-87
    • Paster, B.J.1    Olsen, I.2    Aas, J.A.3    Dewhirst, F.E.4
  • 27
    • 33947238287 scopus 로고    scopus 로고
    • The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific
    • Rusch, D.B., Halpern, A.L., Sutton, G. et al. (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77.
    • (2007) PLoS Biol , vol.5
    • Rusch, D.B.1    Halpern, A.L.2    Sutton, G.3
  • 30
    • 69549086653 scopus 로고    scopus 로고
    • Functional characterization of the antibiotic resistance reservoir in the human microflora
    • Sommer, M.O., Dantas, G. and Church, G.M. (2009) Functional characterization of the antibiotic resistance reservoir in the human microflora. Science (New York, NY) 325: 1128-1131.
    • (2009) Science (New York, NY) , vol.325 , pp. 1128-1131
    • Sommer, M.O.1    Dantas, G.2    Church, G.M.3
  • 31
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, UK) 22: 2688-2690.
    • (2006) Bioinformatics (Oxford, UK) , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 32
    • 33644692952 scopus 로고    scopus 로고
    • Metagenomics: DNA sequencing of environmental samples
    • Tringe, S.G. and Rubin, E.M. (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev 6: 805-814.
    • (2005) Nat Rev , vol.6 , pp. 805-814
    • Tringe, S.G.1    Rubin, E.M.2
  • 33
    • 33845874101 scopus 로고    scopus 로고
    • An obesity-associated gut microbiome with increased capacity for energy harvest
    • Turnbaugh, P.J., Ley, R.E., Mahowald, M.A., Magrini, V., Mardis, E.R. and Gordon, J.I. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031.
    • (2006) Nature , vol.444 , pp. 1027-1031
    • Turnbaugh, P.J.1    Ley, R.E.2    Mahowald, M.A.3    Magrini, V.4    Mardis, E.R.5    Gordon, J.I.6
  • 34
    • 55649110049 scopus 로고    scopus 로고
    • A simple, fast, and accurate method of phylogenomic inference
    • Wu, M. and Eisen, J.A. (2008) A simple, fast, and accurate method of phylogenomic inference. Genome Biol 9: R151.
    • (2008) Genome Biol , vol.9
    • Wu, M.1    Eisen, J.A.2
  • 35
    • 33947235074 scopus 로고    scopus 로고
    • The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families
    • Yooseph, S., Sutton, G., Rusch, D.B. et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5: e16.
    • (2007) PLoS Biol , vol.5
    • Yooseph, S.1    Sutton, G.2    Rusch, D.B.3
  • 36
    • 74949134895 scopus 로고    scopus 로고
    • Defining the healthy 'core microbiome' of oral microbial communities
    • Zaura, E., Keijser, B.J., Huse, S.M. and 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
  • 37
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D.R. and Birney, E. (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 38
    • 77955902981 scopus 로고    scopus 로고
    • Ab initio gene identification in metagenomic sequences
    • Zhu, W., Lomsadze, A. and Borodovsky, M. (2010) Ab initio gene identification in metagenomic sequences. Nucleic Acids Res 38: e132. Doi:
    • (2010) Nucleic Acids Res , vol.38
    • Zhu, W.1    Lomsadze, A.2    Borodovsky, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.