Exploring the oral bacterial flora: Current status and future directions

Oral Diseases

Volumn 16, Issue 2, 2010, Pages 136-145

  Parahitiyawa, N B ^a   Scully, C ^c   Leung, W K ^a   Yam, W C ^b   Jin, L J ^a   Samaranayake, L P ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Immunology and microbiology

Indexed keywords

ARCHAEBACTERIUM; BACTERIAL FLORA; BACTERIAL INFECTION; BACTERIUM IDENTIFICATION; DENTAL CARIES; ENDODONTICS; HUMAN; IMMUNOLOGICAL PROCEDURES; METAGENOMICS; MICROSCOPY; MOUTH CAVITY; MOUTH FLORA; MOUTH LESION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PYROSEQUENCING; REVIEW;

BACTERIA; BACTERIOLOGICAL TECHNIQUES; BIODIVERSITY; HUMANS; METAGENOME; METAGENOMICS; MOUTH; MOUTH DISEASES; TOOTH DISEASES;

EID: 77249086715     PISSN: 1354523X     EISSN: 16010825     Source Type: Journal    
DOI: 10.1111/j.1601-0825.2009.01607.x     Document Type: Review

References (76)

1. Aas JA, Paster BJ, Stokes LN et al (2005). Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43 : 5721 5732.
2. Aas JA, Barbuto SM, Alpagot T et al (2007). Subgingival plaque microbiota in HIV positive patients. J Clin Periodontol 34 : 189 195.
3. Aas JA, Griffen AL, Dardis SR et al (2008). Bacteria of dental caries in primary and permanent teeth in children and young adults. J Clin Microbiol 46 : 1407 1417.
4. Barken KB, Haagensen JA, Tolker-Nielsen T (2007). Advances in nucleic acid-based diagnostics of bacterial infections. Clin Chim Acta 384 : 1 11.
5. Beighton D, Gilbert SC, Clark D et al (2008). Isolation and identification of bifidobacteriaceae from human saliva. Appl Environ Microbiol 74 : 6457 6460.
6. Belay N, Johnson R, Rajagopal BS et al (1988). Methanogenic bacteria from human dental plaque. Appl Environ Microbiol 54 : 600 603.
7. Chhour KL, Nadkarni MA, Byun R et al (2005). Molecular analysis of microbial diversity in advanced caries. J Clin Microbiol 43 : 843 849.
8. Chu FC, Tsang CS, Chow TW, Samaranayake LP (2005). Identification of cultivable microorganisms from primary endodontic infections with exposed and unexposed pulp space. J Endod 31 : 424 429.
9. Chu FC, Leung WK, Tsang PC et al (2006). Identification of cultivable microorganisms from root canals with apical periodontitis following two-visit endodontic treatment with antibiotics/steroid or calcium hydroxide dressings. J Endod 32 : 17 23.
10. D'Ercole S, Catamo G, Piccolomini R (2008). Diagnosis in periodontology: a further aid through microbiological tests. Crit Rev Microbiol 34 : 33 41.
11. Dewhirst FE, Paster BJ, Tzellas N et al (2001). Characterization of novel human oral isolates and cloned 16S rDNA sequences that fall in the family Coriobacteriaceae: description of olsenella gen. nov., reclassification of Lactobacillus uli as Olsenella uli comb. nov. and description of Olsenella profusa sp. nov. Int J Syst Evol Microbiol 51 : 1797 1804.
12. Downes J, Munson MA, Radford DR et al (2002). Shuttleworthia satelles gen. nov., sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 52 : 1469 1475.
13. Downes J, Munson M, Wade WG (2003). Dialister invisus sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 53 : 1937 1940.
14. Downes J, Sutcliffe I, Tanner AC, Wade WG (2005). Prevotella marshii sp. nov. and Prevotella baroniae sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 55 : 1551 1555.
15. Dymock D, Weightman AJ, Scully C, Wade WG (1996). Molecular analysis of microflora associated with dentoalveolar abscesses. J Clin Microbiol 34 : 537 542.
16. Etoh Y, Dewhirst FE, Paster BJ et al (1993). Campylobacter showae sp. nov., isolated from the human oral cavity. Int J Syst Bacteriol 43 : 631 639.
17. Finegold SM, Vaisanen ML, Rautio M et al (2004). Porphyromonas uenonis sp. nov., a pathogen for humans distinct from P. asaccharolytica and P. endodontalis. J Clin Microbiol 42 : 5298 5301.
18. Fujimoto C, Maeda H, Kokeguchi S et al (2003). Application of denaturing gradient gel electrophoresis (DGGE) to the analysis of microbial communities of subgingival plaque. J Periodontal Res 38 : 440 445.
19. Han XY, Hong T, Falsen E (2006). Neisseria bacilliformis sp. nov. isolated from human infections. J Clin Microbiol 44 : 474 479.
20. Hook EW III., Roddy RE, Lukehart SA et al (1985). Detection of Treponema pallidum in lesion exudate with a pathogen-specific monoclonal antibody. J Clin Microbiol 22 : 241 244.
21. Hooper SJ, Crean SJ, Lewis MA et al (2006). Viable bacteria present within oral squamous cell carcinoma tissue. J Clin Microbiol 44 : 1719 1725.
22. Huyghe A, Francois P, Charbonnier Y et al (2008). Novel microarray design strategy to study complex bacterial communities. Appl Environ Microbiol 74 : 1876 1885.
23. Huys G, Vancanneyt M, D'Haene K et al (2007). Alloscardovia omnicolens gen. nov., sp. nov., from human clinical samples. Int J Syst Evol Microbiol 57 : 1442 1446.
24. Jacinto RC, Gomes BP, Desai M et al (2007). Bacterial examination of endodontic infections by clonal analysis in concert with denaturing high-performance liquid chromatography. Oral Microbiol Immunol 22 : 403 410.
25. Jenkinson HF, Lamont RJ (2005). Oral microbial communities in sickness and in health. Trends Microbiol 13 : 589 595.
26. Kazor CE, Mitchell PM, Lee AM et al (2003). Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients. J Clin Microbiol 41 : 558 563.
27. Keijser BJ, Zaura E, Huse SM et al (2008). Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res 87 : 1016 1020.
28. Kikuta N, Yamamoto A, Fukura K, Goto N (1997). Specific and sensitive detection of Trichomonas tenax by the polymerase chain reaction. Lett Appl Microbiol 24 : 193 197.
29. Kroes I, Lepp PW, Relman DA (1999). Bacterial diversity within the human subgingival crevice. Proc Natl Acad Sci USA 96 : 14547 14552.
30. Kulik EM, Sandmeier H, Hinni K, Meyer J (2001). Identification of archaeal rDNA from subgingival dental plaque by PCR amplification and sequence analysis. FEMS Microbiol Lett 196 : 129 133.
31. Kumar PS, Griffen AL, Barton JA et al (2003). New bacterial species associated with chronic periodontitis. J Dent Res 82 : 338 344.
32. Kuramitsu HK, He X, Lux R et al (2007). Interspecies interactions within oral microbial communities. Microbiol Mol Biol Rev 71 : 653 670.
33. Langendijk PS, Kulik EM, Sandmeier H et al (2001). Isolation of Desulfomicrobium orale sp. nov. and Desulfovibrio strain NY682, oral sulfate-reducing bacteria involved in human periodontal disease. Int J Syst Evol Microbiol 51 : 1035 1044.
34. Ledder RG, Gilbert P, Huws SA et al (2007). Molecular analysis of the subgingival microbiota in health and disease. Appl Environ Microbiol 73 : 516 523.
35. Lepp PW, Brinig MM, Ouverney CC et al (2004). Methanogenic Archaea and human periodontal disease. Proc Natl Acad Sci USA 101 : 6176 6181.
36. Li Y, Ge Y, Saxena D, Caufield PW (2007). Genetic profiling of the oral microbiota associated with severe early-childhood caries. J Clin Microbiol 45 : 81 87.
37. de Lillo A, Ashley FP, Palmer RM et al (2006). Novel subgingival bacterial phylotypes detected using multiple universal polymerase chain reaction primer sets. Oral Microbiol Immunol 21 : 61 68.
38. Machado de Oliveira JC, Siqueira JF Jr., Rocas IN et al (2007). Bacterial community profiles of endodontic abscesses from Brazilian and USA subjects as compared by denaturing gradient gel electrophoresis analysis. Oral Microbiol Immunol 22 : 14 18.
39. Macuch PJ, Tanner AC (2000). Campylobacter species in health, gingivitis, and periodontitis. J Dent Res 79 : 785 792.
40. Marchini L, Campos MS, Silva AM et al (2007). Bacterial diversity in aphthous ulcers. Oral Microbiol Immunol 22 : 225 231.
41. Marcy Y, Ouverney C, Bik EM et al (2007). Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci USA 104 : 11889 11894.
42. Munson MA, Banerjee A, Watson TF, Wade WG (2004). Molecular analysis of the microflora associated with dental caries. J Clin Microbiol 42 : 3023 3029.
43. Nakazawa F, Poco SE, Ikeda T et al (1999). Cryptobacterium curtum gen. nov., sp. nov., a new genus of gram-positive anaerobic rod isolated from human oral cavities. Int J Syst Bacteriol 49 (Pt 3 1193 1200.
44. Nakazawa F, Poco SE Jr., Sato M et al (2002). Taxonomic characterization of Mogibacterium diversum sp. nov. and Mogibacterium neglectum sp. nov., isolated from human oral cavities. Int J Syst Evol Microbiol 52 : 115 122.
45. Parahitiyawa NB, Jin LJ, Leung WK et al (2009). Microbiology of odontogenic bacteremia: beyond endocarditis. Clin Microbiol Rev 22 : 46 64.
46. Paster BJ, Boches SK, Galvin JL et al (2001). Bacterial diversity in human subgingival plaque. J Bacteriol 183 : 3770 3783.
47. Preza D, Olsen I, Aas JA et al (2008). Bacterial profiles of root caries in elderly patients. J Clin Microbiol 46 : 2015 2021.
48. Pussinen PJ, Vilkuna-Rautiainen T, Alfthan G et al (2002). Multiserotype enzyme-linked immunosorbent assay as a diagnostic aid for periodontitis in large-scale studies. J Clin Microbiol 40 : 512 518.
49. Rasiah IA, Wong L, Anderson SA, Sissons CH (2005). Variation in bacterial DGGE patterns from human saliva: over time, between individuals and in corresponding dental plaque microcosms. Arch Oral Biol 50 : 779 787.
50. Rocas IN, Siqueira JF Jr. (2005) Occurrence of two newly named oral treponemes - Treponema parvum and Treponema putidum - in primary endodontic infections Oral Microbiol Immunol 20 : 372 375.
51. Rocas IN, Siqueira JF Jr. (2006) Characterization of Dialister species in infected root canals J Endod 32 : 1057 1061.
52. Rocas IN, Siqueira JF Jr. (2008) Root canal microbiota of teeth with chronic apical periodontitis J Clin Microbiol 46 : 3599 3606.
53. Rocas IN, Hulsmann M, Siqueira JF Jr. (2008). Microorganisms in root canal-treated teeth from a German population. J Endod 34 : 926 931.
54. Sakamoto M, Huang Y, Ohnishi M et al (2004) Changes in oral microbial profiles after periodontal treatment as determined by molecular analysis of 16S rRNA genes J Med Microbiol 53 : 563 571.
55. Sakamoto M, Huang Y, Umeda M et al (2005a) Prevotella multiformis sp nov, isolated from human subgingival plaque Int J Syst Evol Microbiol 55 : 815 819. (Pubitemid 40485076)
56. Sakamoto M, Umeda M, Ishikawa I, Benno Y (2005b). Prevotella multisaccharivorax sp nov, isolated from human subgingival plaque. Int J Syst Evol Microbiol 55 : 1839 1843. (Pubitemid 41410392)
57. Sakamoto M, Siqueira JF Jr., Rocas IN, Benno Y (2007). Bacterial reduction and persistence after endodontic treatment procedures. Oral Microbiol Immunol 22 : 19 23.
58. Sakamoto M, Siqueira JF Jr., Rocas IN, Benno Y (2009). Diversity of spirochetes in endodontic infections. J Clin Microbiol 47 : 1352 1357.
59. Samaranayake LP (2006a). Microbiology of periodontal disease. Essential microbiology for dentistry, 3rd edn. Elsevier : Philadelphia, pp. 275 285.
60. Samaranayake LP (2006b). Normal oral flora, the oral ecosystem and plaque biofilm. Essential microbiology for dentistry. Elsevier : Philadelphia, pp. 255 266.
61. Samaranayake LP (2006c). Normal oral flora, the oral ecosystem and plaque biofilms. Essential microbiology for dentistry, 3rd edn. Elsevier : Philadelphia, pp. 255 266.
62. Schirrmeister JF, Liebenow AL, Pelz K et al (2009). New bacterial compositions in root-filled teeth with periradicular lesions. J Endod 35 : 169 174.
63. Siqueira JF Jr., Rocas IN (2003). PCR-based identification of Treponema maltophilum, T amylovorum, T medium, and T lecithinolyticum in primary root canal infections. Arch Oral Biol 48 : 495 502.
64. Siqueira JF Jr., Rocas IN (2005). Uncultivated phylotypes and newly named species associated with primary and persistent endodontic infections. J Clin Microbiol 43 : 3314 3319.
65. Siqueira JF Jr., Rocas IN (2009). The microbiota of acute apical abscesses. J Dent Res 88 : 61 65.
66. Turnbaugh PJ, Ley RE, Hamady M et al (2007). The human microbiome project. Nature 449 : 804 810.
67. Vianna ME, Conrads G, Gomes BP, Horz HP (2006). Identification and quantification of archaea involved in primary endodontic infections. J Clin Microbiol 44 : 1274 1282.
68. Vickerman MM, Brossard KA, Funk DB et al (2007). Phylogenetic analysis of bacterial and archaeal species in symptomatic and asymptomatic endodontic infections. J Med Microbiol 56 : 110 118.
69. Wade WG, Spratt DA, Dymock D, Weightman AJ (1997). Molecular detection of novel anaerobic species in dentoalveolar abscesses. Clin Infect Dis 25 (Suppl 2 S235 S236.
70. Woese CR, Kandler O, Wheelis ML (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87 : 4576 4579.
71. Wommack KE, Bhavsar J, Ravel J (2008). Metagenomics: read length matters. Appl Environ Microbiol 74 : 1453 1463.
72. Woo PC, Lau SK, Teng JL et al (2008). Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect 14 : 908 934.
73. Wyss C, Choi BK, Schupbach P et al (1996). Treponema maltophilum sp nov, a small oral spirochete isolated from human periodontal lesions. Int J Syst Bacteriol 46 : 745 752.
74. Wyss C, Choi BK, Schupbach P et al (1999) Treponema lecithinolyticum sp nov, a small saccharolytic spirochaete with phospholipase A and C activities associated with periodontal diseases. Int J Syst Bacteriol 49 (Pt 4 1329 1339.
75. Wyss C, Dewhirst FE, Gmur R et al (2001). Treponema parvum sp nov, a small, glucoronic or galacturonic acid-dependent oral spirochaete from lesions of human periodontitis and acute necrotizing ulcerative gingivitis. Int J Syst Evol Microbiol 51 : 955 962.
76. Wyss C, Moter A, Choi BK et al (2004). Treponema putidum sp nov, a medium-sized proteolytic spirochaete isolated from lesions of human periodontitis and acute necrotizing ulcerative gingivitis. Int J Syst Evol Microbiol 54 : 1117 1122.