Investigation of bacterial communities associated with asymptomatic and symptomatic endodontic infections by denaturing gradient gel electrophoresis fingerprinting approach

Oral Microbiology and Immunology

Volumn 19, Issue 6, 2004, Pages 363-370

  Siqueira Jr , José F ^a,b,c   Rocas I N ^a   Rosado, A S ^b  

^a ESTÁCIO DE SÁ UNIVERSITY   (Brazil)

^b FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^c NONE   (Brazil)

Author keywords

16S rRNA gene; Endodontic microbiology; Molecular biology; Symptoms

Indexed keywords

DNA 16S;

ACINETOBACTER; ARTICLE; BACTERIAL FLORA; CAMPYLOBACTER; CHROMOSOME HIGH RESOLUTION BANDING ANALYSIS; COMPARATIVE STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA EXTRACTION; DNA FINGERPRINTING; ENTEROBACTERIACEAE; FUSOBACTERIUM; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRINCIPAL COMPONENT ANALYSIS; SYMPTOMATOLOGY; TOOTH INFECTION; TOOTH ROOT CANAL;

ACINETOBACTER; ADULT; AGED; BACTERIAL INFECTIONS; BACTERIAL TYPING TECHNIQUES; CAMPYLOBACTER; CLUSTER ANALYSIS; DENTAL PULP DISEASES; DNA FINGERPRINTING; DNA, BACTERIAL; ECOSYSTEM; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ENTEROBACTERIACEAE; FUSOBACTERIUM; HUMANS; MIDDLE AGED; PRINCIPAL COMPONENT ANALYSIS; PROTEIN DENATURATION; SEQUENCE ANALYSIS, DNA; TOOTHACHE;

EID: 8444239642     PISSN: 09020055     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1399-302x.2004.00170.x     Document Type: Article

References (42)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990: 215: 403-410.
2. Baumgartner JC, Watkins BJ, Bae KS, Xia T. Association of black-pigmented bacteria with endodontic infections. J Endod 1999: 25: 413-415.
3. Donskey CJ, Hujer AM, Das SM, Pultz NJ, Bonomo RA, Rice LB. Use of denaturing gradient gel electrophoresis for analysis of the stool microbiota of hospitalized patients. J Microbiol Methods 2003: 54: 249-256.
4. Fischer SG, Lerman LS. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc Natl Acad Sci U S A 1983: 80: 1579-1583.
5. Fox GE, Wisotzkey JD, Jurtsuk P. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 1992: 42: 166-170.
6. Fromin N, Hamelin J, Tarnawski S, Roesti D, Jourdain-Miserez K, Forestier N, et al. Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ Microbiol 2002: 4: 634-643.
7. Fujimoto C, Maeda H, Kokeguchi S, Takashiba S, Nishimura F, Arai H, et al. Application of denaturing gradient gel electrophoresis (DGGE) to the analysis of microbial communities of subgingival plaque. J Periodontal Res 2003: 38: 440-445.
8. Gasser RB. What's in that band? Int J Parasitol 1998: 28: 989-996.
9. Gillan DC, Speksnijder AGCL, Zwart G, de Ridder C. Genetic diversity of the biofilm covering Montacuta ferruginosa (Mollusca, Bivalvia) as evaluated by denaturing gradient gel electrophoresis analysis and cloning of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 1998: 64: 3464-3472.
10. Göbel UB. Phylogenetic amplification for the detection of uncultured bacteria and the analysis of complex microbiota. J Microbiol Methods 1995: 23: 117-128.
11. Haapasalo M, Ranta H, Ranta K, Shah H. Black-pigmented Bacteroides spp. in human apical periodontitis. Infect Immun 1986: 53: 149-153.
12. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Series 1999: 41, 95-98.
13. Khemaleelakul S, Baumgartner JC, Pruksakom S. Identification of bacteria in acute endodontic infections and their antimicrobial susceptibility. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2002: 94: 746-755.
14. Kumar S, Tamura K, Jakobsen IB, Nei M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 2001: 17: 1244-1245.
15. Millar MR, Linton CJ, Cade A, Glancy D, Hall M, Jalal H. Application of 16S rRNA gene PCR to study bowel flora of preterm infants with and without necrotizing enterocolitis. J Clin Microbiol 1996: 34: 2506-2510.
16. Moraes SR, Siqueira JF Jr, Colombo AP, Rôças IN, Ferreira MC, Domingues RM. Comparison of the effectiveness of bacterial culture, 16s rDNA directed polymerase chain reaction, and checkerboard DNA-DNA hybridization for detection of Fuso-bacterium nitdeatum in endodontic infections. J Endod 2002: 28: 86-89.
17. Müller AK, Westergaard K, Christensen S, Sorensen SJ. The effect of long-term mercury pollution on the soil microbial community. FEMS Microbiol Ecol 2001: 36: 11-19.
18. Murray AE, Hollibaugh JT, Orrego C. Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl Environ Microbiol 1996: 62: 2676-2680.
19. Muyzer G. DGGE/TGGE: a method for identifying genes from natural ecosystems. Curr Opin Microbiol 1999: 2: 317-322.
20. Muyzer G, de Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 1993: 59: 695-700.
21. Muyzer G, Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 1998: 73: 127-141.
22. Myers RM, Fischer SG, Lerman LS, Maniatis T. Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res 1985: 13: 3131-3145.
23. Myers RM, Maniatis T, Lerman LS. Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol 1987: 155: 501-527.
24. Nübel U, Engelen B, Felske A, Snaidr J, Wieshuber A, Amann RI, et al. Sequence heterogeneities of genes encoding 16S rRNAs in PaenibaciUus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 1996: 178: 5636-5643.
25. Rudney JD, Pan Y, Chen R. Streptococcal diversity in oral biofilms with respect to salivary function. Arch Oral Biol 2003: 48: 475-493.
26. Schabereiter-Gurtner C, Maca S, Kaminsky S, Rölleke S, Lubitz W, Barisani-Asenbauer T. Investigation of an anaerobic microbial community associated with a corneal ulcer by denaturing gradient gel electrophoresis and 16S rDNA sequence analysis. Diagn Microbiol Infect Dis 2002: 43: 193-199.
27. Siqueira JF Jr. Endodontic infections: concepts, paradigms and perspectives. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2002: 94: 281-293.
28. Siqueira JF Jr. Microbial causes of endodontic flare-ups. Int Endod J 2003: 36: 453-463.
29. Siqueira JF Jr. Taxonomic changes of bacteria associated with endodontic infections. J Endod 2003: 29: 619-623.
30. Siqueira JF Jr, Rôças IN. Campylobacter gracilis and Campylobacter rectus in primary endodontic infections. Int Endod J 2003: 36: 174-180.
31. Siqueira JF Jr, Rôças IN, Oliveira JCM, Santos KRN. Molecular detection of black-pigmented bacteria in infections of endodontic origin. J Endod 2001: 27: 563-566.
32. Siqueira JF Jr, Rôças IN, Souto R, Uzeda M, Colombo AP. Checkerboard DNA-DNA hybridization analysis of endodontic infections. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2000: 89: 744-748.
33. Siqueira JF Jr, Rôças IN, Souto R, Uzeda M, Colombo AP. Microbiological evaluation of acute periradicular abscesses by DNA-DNA hybridization. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2001: 92: 451-457.
34. Sousa ELR, Ferraz CCR, Gomes BPF, Pinheiro ET, Teixeira FB, Souza-Filho FJ. Bacteriological study of root canals associated with periapical abscesses. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2003: 96: 332-339.
35. Sundqvist G. Associations between microbial species in dental root canal infections. Oral Microbiol Immunol 1992: 7: 257-262.
36. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997: 24: 4876-4882.
37. van der Gucht K, Sabbe K, de Meester L, Vloemens N, Zwart G, Gillis M, et al. Contrasting bacterioplankton community composition and seasonal dynamics in two neighbouring hypertrophie freshwater lakes. Environ Microbiol 2001: 3: 680-690.
38. Walter J, Hertel C, Tannock GW, Lis CM, Munro K, Hammes WP. Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denaturing gradient gel electrophoresis. Appl Environ Microbiol 2001: 67: 2578-2585.
39. Wintzingerode FV, Göbel UB, Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 1997: 21: 213-229.
40. Yang C-H, Crowley DE, Menge JA. 16S rDNA fingerprinting of rhizosphere bacterial communities associated with healthy and Phytophthora infected avocado roots. FEMS Microbiol Ecol 2001: 35: 129-136.
41. Zijnge V, Harmsen HJ, Kleinfelder JW, van der Rest ME, Degener JE, Welling GW. Denaturing gradient gel electrophoresis analysis to study bacterial community structure in pockets of periodontitis patients. Oral Microbiol Immunol 2003: 18: 59-65.
42. Zoetendal EG, von Wright A, Vilpponen-Salmela T, Ben-Amor K, Akkermans ADL, de Vos WM. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 2002: 68: 3401-3407.