The Human Oral Metagenome

The human oral cavity is estimated to contain more than 750 bacterial species (Jenkinson and Lamont, 2005; Paster et al., 2006). Although this figure is controversial, the fact remains that up to half of the species in the oral microbiota cannot yet be cultivated in the laboratory. Therefore, metagenomics is a powerful way of accessing these unculturable bacteria in order to understand the role of the oral microbiota in health and disease and to mine for useful products such as enzymes, energy sources and antimicrobial agents. The Human Oral Microbiome Database (HOMD http://www.homd.org/) provides comprehensive information on what is known about the composition of the oral microbiota using information derived from cultivation and metagenomic data based on 16S rRNA gene sequencing.

[1]  D. Clermont,et al.  Natural occurrence of structures in oral streptococci and enterococci with DNA homology to Tn916 , 1992, Antimicrobial Agents and Chemotherapy.

[2]  R. Lamont,et al.  LuxS-Based Signaling in Streptococcus gordonii: Autoinducer 2 Controls Carbohydrate Metabolism and Biofilm Formation with Porphyromonas gingivalis , 2003, Journal of bacteriology.

[3]  W. Wade,et al.  Demonstration of in vivo transfer of doxycycline resistance mediated by a novel transposon. , 2007, The Journal of antimicrobial chemotherapy.

[4]  D. Ojcius,et al.  The oral microbiota: living with a permanent guest. , 2009, DNA and cell biology.

[5]  K. R. Jones,et al.  Disseminated tetracycline resistance in oral streptococci: implication of a conjugative transposon , 1984, Infection and immunity.

[6]  C. Walsh.  Molecular mechanisms that confer antibacterial drug resistance , 2000, Nature.

[7]  Peter Mullany,et al.  A modular master on the move: the Tn916 family of mobile genetic elements. , 2009, Trends in microbiology.

[8]  M. Parsek,et al.  Quorum sensing and microbial biofilms. , 2008, Current topics in microbiology and immunology.

[9]  D. Crook,et al.  Genomic islands: tools of bacterial horizontal gene transfer and evolution , 2008, FEMS microbiology reviews.

[10]  J. V. D. Ploeg,et al.  Characterization of Streptococcus gordonii prophage PH15: complete genome sequence and functional analysis of phage-encoded integrase and endolysin. , 2008 .

[11]  Eric R. Houpt,et al.  Microbial Inhabitants of Humans: Their Ecology and Role in Health and Disease:Microbial Inhabitants of Humans: Their Ecology and Role in Health and Disease , 2004 .

[12]  N. Slakeski,et al.  Treponema denticola biofilm-induced expression of a bacteriophage, toxin-antitoxin systems and transposases. , 2010, Microbiology.

[13]  Bruce J Paster,et al.  Bacteremia Associated With Toothbrushing and Dental Extraction , 2008, Circulation.

[14]  J. Marchesi,et al.  Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome , 2007, Nature Methods.

[15]  Ying Wang,et al.  Identification of a Genomic Island of Actinobacillus actinomycetemcomitans. , 2005, Journal of periodontology.

[16]  Peter Mullany,et al.  Determining the antibiotic resistance potential of the indigenous oral microbiota of humans using a metagenomic approach. , 2006, FEMS microbiology letters.

[17]  P. Harbury,et al.  In vitro selection and prediction of TIP47 protein-interaction interfaces , 2004, Nature Methods.

[18]  A. Edwards,et al.  Association of a high-molecular weight arginine-binding protein of Fusobacterium nucleatum ATCC 10953 with adhesion to secretory immunoglobulin A and coaggregation with Streptococcus cristatus. , 2007, Oral microbiology and immunology.

[19]  P. Lockhart,et al.  Poor oral hygiene as a risk factor for infective endocarditis-related bacteremia. , 2009, Journal of the American Dental Association.

[20]  B. Paster,et al.  Diverse and Novel Oral Bacterial Species in Blood following Dental Procedures , 2008, Journal of Clinical Microbiology.

[21]  T. Griffin,et al.  A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry. , 2010, Molecular oral microbiology.

[22]  R. Lamont,et al.  Streptococcus Adherence and Colonization , 2009, Microbiology and Molecular Biology Reviews.

[23]  D. Beighton,et al.  The complex oral microflora of high-risk individuals and groups and its role in the caries process. , 2005, Community dentistry and oral epidemiology.

[24]  P. Mullany,et al.  Novel Tetracycline Resistance Determinant from the Oral Metagenome , 2003, Antimicrobial Agents and Chemotherapy.

[25]  T. Sutherland,et al.  Global transcriptional analysis of acid-inducible genes in Streptococcus mutans: multiple two-component systems involved in acid adaptation. , 2009, Microbiology.

[26]  J. C. Waterhouse,et al.  Dispensable genes and foreign DNA in Streptococcus mutans. , 2006, Microbiology.

[27]  K. Hojo,et al.  Bacterial Interactions in Dental Biofilm Development , 2009, Journal of dental research.

[28]  P. Taylor,et al.  Isolation of bacteriophages from the oral cavity , 2004, Letters in applied microbiology.

[29]  S. Levy,et al.  Molecular Mechanisms of Antibacterial Multidrug Resistance , 2007, Cell.

[30]  J. A. Aas,et al.  The breadth of bacterial diversity in the human periodontal pocket and other oral sites. , 2006, Periodontology 2000.

[31]  A. Roberts,et al.  Characterization of tet(32) Genes from the Oral Metagenome , 2008, Antimicrobial Agents and Chemotherapy.

[32]  Robert J. Palmer,et al.  Characterization of a Streptococcus sp.-Veillonella sp. Community Micromanipulated from Dental Plaque , 2008, Journal of bacteriology.

[33]  M. Quail,et al.  Distribution of tetracycline and erythromycin resistance genes among human oral and fecal metagenomic DNA. , 2009, Microbial drug resistance.

[34]  Philip D Marsh,et al.  Dental plaque as a biofilm and a microbial community – implications for health and disease , 2006, BMC oral health.

[35]  M. Moeschberger,et al.  Identification of Candidate Periodontal Pathogens and Beneficial Species by Quantitative 16S Clonal Analysis , 2005, Journal of Clinical Microbiology.

[36]  R. Lamont,et al.  Oral microbial communities in sickness and in health. , 2005, Trends in microbiology.

[37]  G. Fichant,et al.  Independent evolution of competence regulatory cascades in streptococci? , 2006, Trends in microbiology.

[38]  P. Chattoraj,et al.  ClpP of Streptococcus mutans Differentially Regulates Expression of Genomic Islands, Mutacin Production, and Antibiotic Tolerance , 2009, Journal of bacteriology.

[39]  G. Church,et al.  Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora , 2009, Science.

[40]  Robert J. Palmer,et al.  Communication among Oral Bacteria , 2002, Microbiology and Molecular Biology Reviews.

[41]  Susan M. Huse,et al.  Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. , 2009, Journal of microbiological methods.

[42]  K. Raghavendran,et al.  Nursing home-associated pneumonia, hospital-acquired pneumonia and ventilator-associated pneumonia: the contribution of dental biofilms and periodontal inflammation. , 2007, Periodontology 2000.