Comparing the bacterial diversity of acute and chronic dental root canal infections

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Santos, Adriana L ^a   Siqueira Jr , José F ^b   Rôças, Isabela N ^b   Jesus, Ederson C ^d   Rosado, Alexandre S ^a   Tiedje, James M ^c  

^a FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^b ESTÁCIO DE SÁ UNIVERSITY   (Brazil)

^c MICHIGAN STATE UNIVERSITY   (United States)

^d EMBRAPA CERRADOS   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ACUTE PERIODONTITIS; ADULT; ARTICLE; BACTERIUM DETECTION; CHRONIC PERIODONTITIS; CLINICAL ARTICLE; CONTROLLED STUDY; ENDODONTICS; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROFLORA; NONHUMAN; OPERATIONAL TAXONOMIC UNIT; PERIODONTITIS; PHYLUM; POPULATION ABUNDANCE; PYROSEQUENCING; SPECIES COMPARISON; SPECIES RICHNESS; TAXONOMY; TOOTH ABSCESS; TOOTH ROOT CANAL; ACUTE DISEASE; ADOLESCENT; BACTERIAL INFECTION; BACTERIUM; BIODIVERSITY; CHRONIC DISEASE; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; GROWTH, DEVELOPMENT AND AGING; MICROBIOLOGY; MIDDLE AGED; PATHOLOGY; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; TOOTH PULP;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; FIRMICUTES; FUSOBACTERIA; FUSOBACTERIUM; OTUS;

ACUTE DISEASE; ADOLESCENT; ADULT; BACTERIA; BACTERIAL INFECTIONS; BIODIVERSITY; CHRONIC DISEASE; CLUSTER ANALYSIS; DENTAL PULP CAVITY; HUMANS; MIDDLE AGED; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA; YOUNG ADULT;

EID: 81455127375     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028088     Document Type: Article

References (53)

1. Siqueira JF Jr, (2011) Treatment of endodontic infections. London Quintessence Publishing.
2. Caplan DJ, Chasen JB, Krall EA, Cai J, Kang S, et al. (2006) Lesions of endodontic origin and risk of coronary heart disease. J Dent Res 85: 996-1000.
3. Robertson D, Smith AJ, (2009) The microbiology of the acute dental abscess. J Med Microbiol 58: 155-162.
4. Siqueira JF Jr, (2002) Endodontic infections: concepts, paradigms, and perspectives. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 94: 281-293.
5. Sundqvist G, (1976) Bacteriological studies of necrotic dental pulps [Odontological Dissertation no.7]. Umea, Sweden University of Umea.
6. Gomes BP, Lilley JD, Drucker DB, (1996) Clinical significance of dental root canal microflora. J Dent 24: 47-55.
7. Siqueira JF Jr, Rôças IN, (2009) The microbiota of acute apical abscesses. J Dent Res 88: 61-65.
8. Baumgartner JC, Watkins BJ, Bae KS, Xia T, (1999) Association of black-pigmented bacteria with endodontic infections. J Endod 25: 413-415.
9. Siqueira JF Jr, Rôças IN, Souto R, de Uzeda M, Colombo AP, (2000) Checkerboard DNA-DNA hybridization analysis of endodontic infections. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 89: 744-748.
10. Rôças IN, Siqueira JF Jr, (2008) Root canal microbiota of teeth with chronic apical periodontitis. J Clin Microbiol 46: 3599-3606.
11. Siqueira JF Jr, Rôças IN, Rosado AS, (2004) Investigation of bacterial communities associated with asymptomatic and symptomatic endodontic infections by denaturing gradient gel electrophoresis fingerprinting approach. Oral Microbiol Immunol 19: 363-370.
12. Sakamoto M, Rôças IN, Siqueira JF Jr, Benno Y, (2006) Molecular analysis of bacteria in asymptomatic and symptomatic endodontic infections. Oral Microbiol Immunol 21: 112-122.
13. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P, (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123.
14. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 103: 12115-12120.
15. Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, et al. (2007) Microbial population structures in the deep marine biosphere. Science 318: 97-100.
16. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AK, et al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1: 283-290.
17. Teixeira LC, Peixoto RS, Cury JC, Sul WJ, Pellizari VH, et al. (2010) Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME J 4: 989-1001.
18. Koren O, Spor A, Felin J, Fak F, Stombaugh J, et al. (2011) Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc Natl Acad Sci U S A 108 (Suppl 1): 4592-4598.
19. Sundquist A, Bigdeli S, Jalili R, Druzin ML, Waller S, et al. (2007) Bacterial flora-typing with targeted, chip-based Pyrosequencing. BMC Microbiol 7: 108.
20. Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, et al. (2010) Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol 10: 206.
21. Dethlefsen L, Huse S, Sogin ML, Relman DA, (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6: e280.
22. Dowd SE, Sun Y, Secor PR, Rhoads DD, Wolcott BM, et al. (2008) Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMC Microbiol 8: 43.
23. Lazarevic V, Whiteson K, Hernandez D, Francois P, Schrenzel J, (2010) Study of inter- and intra-individual variations in the salivary microbiota. BMC Genomics 11: 523.
24. Zaura E, Keijser BJ, Huse SM, Crielaard W, (2009) Defining the healthy "core microbiome" of oral microbial communities. BMC Microbiol 9: 259.
25. Nasidze I, Quinque D, Li J, Li M, Tang K, et al. (2009) Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches. Anal Biochem 391: 64-68.
26. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, et al. (2008) Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res 87: 1016-1020.
27. Li L, Hsiao WW, Nandakumar R, Barbuto SM, Mongodin EF, et al. (2010) Analyzing endodontic infections by deep coverage pyrosequencing. J Dent Res 89: 980-984.
28. Siqueira JF Jr, Alves FR, Rôças IN, (2011) Pyrosequencing analysis of the apical root canal microbiota. J Endod 37: 1499-1503.
29. Siqueira JF Jr, Rôças IN, (2009) Community as the unit of pathogenicity: an emerging concept as to the microbial pathogenesis of apical periodontitis. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 107: 870-878.
30. Kuramitsu HK, He X, Lux R, Anderson MH, Shi W, (2007) Interspecies interactions within oral microbial communities. Microbiol Mol Biol Rev 71: 653-670.
31. Costerton JW, (2007) The biofilm primer. Berlin, Heidelberg Springer-Verlag.
32. Haapasalo M, Ranta H, Ranta K, Shah H, (1986) Black-pigmented Bacteroides spp. in human apical periodontitis. Infect Immun 53: 149-153.
33. Siqueira JF Jr, Rôças IN, Debelian GJ, Carmo FL, Paiva SS, et al. (2008) Profiling of root canal bacterial communities associated with chronic apical periodontitis from Brazilian and Norwegian subjects. J Endod 34: 1457-1461.
34. Machado de Oliveira JC, Siqueira JF Jr, Rôças IN, Baumgartner JC, Xia T, 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.
35. Siqueira JF Jr, Rôças IN, (2009) Diversity of endodontic microbiota revisited. J Dent Res 88: 969-981.
36. Sundqvist G, (1992) Associations between microbial species in dental root canal infections. Oral Microbiol Immunol 7: 257-262.
37. Munson MA, Pitt-Ford T, Chong B, Weightman A, Wade WG, (2002) Molecular and cultural analysis of the microflora associated with endodontic infections. J Dent Res 81: 761-766.
38. Chavez de Paz LE, (2002) Fusobacterium nucleatum in endodontic flare-ups. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 93: 179-183.
39. Williams BL, McCann GF, Schoenknecht FD, (1983) Bacteriology of dental abscesses of endodontic origin. J Clin Microbiol 18: 770-774.
40. Sundqvist G, Johansson E, Sjogren U, (1989) Prevalence of black-pigmented bacteroides species in root canal infections. J Endod 15: 13-19.
41. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 103: 12115-12120.
42. Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA, et al. (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 4: e1000255.
43. Schloss PD, Handelsman J, (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.
44. Rajilic-Stojanovic M, Smidt H, de Vos WM, (2007) Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 9: 2125-2136.
45. Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Relman DA, et al. (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 4: e1000255.
46. 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.
47. 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.
48. 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.
49. Jukes TH, Cantor CR, (1969) Evolution of protein molecules. In: Unro HNM, editors. Mammalian protein metabolism New York Academic Press pp. 21-132.
50. Chao A, Bunge J, (2002) Estimating the number of species in a stochastic abundance model. Biometrics 58: 531-539.
51. Shannon CE, Weaver W, (1949) The mathematical theory of communications. Urbana University of Illinois Press.
52. Kindt R, Coe R, (2005) Tree diversity analysis. A manual and software for common statistical methods and biodiversity studies. Nairobi World Agroforestry Centre (ICRAF).
53. Oksanen J, Blanchet FG, Kindt R, Legendre P, O'Hara RB, et al. (2011) Vegan: Community Ecology Package. R package version 1.17-6. The Comprehensive R Archive Network website. http://CRAN.R-project.org/package=vegan. Accessed 2011 Apr 21.