Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

BMC Microbiology

Volumn 11, Issue , 2011, Pages

  Quevedo, Beatrice ^a   Giertsen, Elin ^b   Zijnge, Vincent ^c   Lüthi Schaller, Helga ^a   Guggenheim, Bernhard ^a   Thurnheer, Thomas ^a   Gmür, Rudolf ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b UNIVERSITY OF OSLO   (Norway)

^c UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ACHROMOPEPTIDASE; LYSOZYME; PEPTIDASE; RNA 16S; TRIACYLGLYCEROL LIPASE; UNCLASSIFIED DRUG; BACTERIAL DNA;

ABIOTROPHIA; ARTICLE; BACTERIUM DETECTION; BIOFILM; CELL MEMBRANE PERMEABILITY; ENAMEL; FLUORESCENCE IN SITU HYBRIDIZATION; GRANULICATELLA; LACTIC ACID BACTERIUM; LACTOBACILLUS CASEI; LACTOBACILLUS FERMENTUM; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; PHYLOGENETIC TREE; PHYLOGENY; STREPTOCOCCUS; STREPTOCOCCUS MUTANS; ANIMAL; CATTLE; GENETICS; HUMAN; ISOLATION AND PURIFICATION; LACTOBACILLACEAE; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; MOUTH; SINGLE CELL ANALYSIS; SPECIES DIFFERENCE; TOOTH PLAQUE;

BOVINAE; LACTOBACILLUS CASEI; LACTOBACILLUS FERMENTUM; STREPTOCOCCUS MUTANS;

ABIOTROPHIA; ANIMALS; BASE SEQUENCE; BIOFILMS; CATTLE; DENTAL PLAQUE; DNA, BACTERIAL; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; LACTOBACILLACEAE; MOLECULAR SEQUENCE DATA; MOUTH; OLIGONUCLEOTIDE PROBES; PHYLOGENY; RNA, RIBOSOMAL, 16S; SINGLE-CELL ANALYSIS; SPECIES SPECIFICITY; STREPTOCOCCUS MUTANS;

EID: 78651486322     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-11-14     Document Type: Article

References (40)

1. Defining the normal bacterial flora of the oral cavity. JA Aas BJ Paster LN Stokes I Olsen FE Dewhirst, J Clin Microbiol 2005 43 5721 5732 10.1128/JCM.43.11.5721-5732.2005 16272510
2. Streptococcus and Lactobacillus. M Kilian, Topley and Wilson's Microbiology and Microbial Infections London: Hodder Arnold, Borriello P, Murray PR, Funke G, 2005 833 881
3. PD Marsh MV Martin, Oral Microbiology Edinburgh: Churchill Livingstone Elsevier 5 2009
4. The oral microflora and biofilms on teeth. PD Marsh B Nyvad, Dental Caries: The Disease and Its Clinical Management UK: Wiley-Blackwell, Fejerskov O, Kidd E. Chichester, 2 2008 163 187
5. Virulence factors among gram-positive bacteria in experimental endocarditis. LM Baddour, Infect Immun 1994 62 2143 2148 8188334
6. Lactobacillus bacterimia and endocarditis: Review of 45 cases. RN Husni SM Gordon JA Washington DL Longworth, Clin Infect Dis 1997 25 1048 1055 10.1086/516109 9402355
7. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. R Amann BM Fuchs, Nat Rev Micro 2008 6 339 348 10.1038/nrmicro1888 (Pubitemid 351552655)
8. Oral biofilm architecture on natural teeth. V Zijnge MBM van Leeuwen JE Degener F Abbas T Thurnheer R Gmür HJM Harmsen, PLoS ONE 2010 5 9321 10.1371/journal.pone.0009321 20195365
9. A 16S rRNA-targeted probe for detection of lactobacilli and enterococci in faecal samples by fluorescent in situ hybridization. HJM Harmsen P Elfferich F Schut GW Welling, Microb Ecol Health Dis 1999 11 3 12 10.1080/089106099435862 (Pubitemid 29248950)
10. Automated fluorescent in situ hybridization for the specific detection and quantification of oral streptococci in dental plaque. T Thurnheer R Gmür E Giertsen B Guggenheim, J Microbiol Methods 2001 44 39 47 10.1016/S0167-7012(00)00226-8 11166098
11. The human oral microbiome database. http://www.HOMD.org
12. The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. T Chen WH Yu J Izard OV Baranova A Lakshmanan FE Dewhirst, Database (Oxford) 2010 2010 aq013 20624719
13. Specific oligonucleotide probes for in situ detection of a major group of gram-positive bacteria with low DNA G+C content. H Meier R Amann W Ludwig KH Schleifer, System Appl Microbiol 1999 22 186 196
14. Phylogenetic oligonucleotide probes for the major subclasses of proteobacteria: problems and solutions. W Manz R Amann W Ludwig M Wagner KH Schleifer, System Appl Microbiol 1992 15 593 600
15. Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. BM Fuchs FO Glöckner J Wulf R Amann, Appl Environ Microbiol 2000 66 3603 3607 10.1128/AEM.66.8.3603-3607.2000 10919826
16. Improved in situ hybridization efficiency with locked-nucleic-acid- incorporated DNA probes. K Kubota A Ohashi H Imachi H Harada, Appl Environ Microbiol 2006 72 5311 5317 10.1128/AEM.03039-05 16885281
17. Selection of dairy bacterial strains as probiotics for oral health. EM Comelli B Guggenheim F Stingele JR Neeser, Eur J Oral Sci 2002 110 218 224 10.1034/j.1600-0447.2002.21216.x 12120707
18. Microbiological aspects of an in situ model to study effects of antimicrobial agents on dental plaque ecology. E Giertsen B Guggenheim T Thurnheer R Gmür, Eur J Oral Sci 2000 108 403 411 10.1034/j.1600-0722.2000. 108005403.x 11037756
19. Bacterial composition and red fluorescence of plaque in relation to primary and secondary caries next to composite: an in situ study. RZ Thomas HC van der Mei MH van der Veen JJ de Soet MCDNJM Huysmans, Oral Microbiol Immunol 2008 23 7 13 10.1111/j.1399-302X.2007.00381.x 18173792
20. Genetic approaches to the identification of the mitis group within the genus Streptococcus. Y Kawamura RA Whiley SE Shu T Ezaki JM Hardie, Microbiology 1999 145 2605 2613 10517614
21. Evolution of Streptococcus pneumoniae and its close commensal relatives. M Kilian K Poulsen T Blomqvist LS Håvarstein M Bek-Thomsen H Tettelin UBS Sørensen, PLoS ONE 2008 3 2683 10.1371/journal.pone.0002683 18628950
22. Further limitations of phylogenetic group-specific probes used for detection of bacteria in environmental samples. JJ Barr LL Blackall B Philip, ISME J 2010 4 1 3 10.1038/ismej.2010.37 19587773
23. Characterization of Actinomyces with genomic DNA fingerprints and rRNA gene probes. G Bowden J Johnson C Schachtele, J Dent Res 1993 72 1171 1179 10.1177/00220345930720080201 8360358
24. An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. R Sekar A Pernthaler J Pernthaler F Warnecke T Posch R Amann, Appl Environ Microbiol 2003 69 2928 2935 10.1128/AEM.69.5. 2928-2935.2003 12732568
25. In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. S Behrens C Rühland J Inacio H Huber A Fonseca I Spencer-Martins BM Fuchs R Amann, Appl Environ Microbiol 2003 69 1748 1758 10.1128/AEM.69.3.1748-1758.2003 12620867 (Pubitemid 36314318)
26. Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides. LS Yilmaz HE Okten DR Noguera, Appl Environ Microbiol 2006 72 733 744 10.1128/AEM.72.1.733-744.2006 16391113
27. A combined immunofluorescence and fluorescent in situ hybridization assay for single cell analyses of dental plaque microorganisms. R Gmür H Lüthi-Schaller, J Microbiol Methods 2007 69 402 405 17258338
28. Antigenic heterogeneity of Bacteroides intermedius as recognized by monoclonal antibodies. R Gmür B Guggenheim, Infect Immun 1983 42 459 470 6196291
29. In vitro quantitative light-induced fluorescence to measure changes in enamel mineralization. R Gmür E Giertsen MH van der Veen E de Josselin de Jong JM ten Cate B Guggenheim, Clin Oral Invest 2006 10 187 195
30. Uncultivated Tannerella BU045 and BU063 are slim segmented filamentous rods of high prevalence but low abundance in inflammatory disease-associated dental plaques. J Züger H Lüthi-Schaller R Gmür, Microbiology 2007 153 3817 3829 17975091
31. ARB: a software environment for sequence data. W Ludwig O Strunk R Westram L Richter H Meier A Yadhukumar Buchner T Lai S Steppi G Jobb W Förster I Brettske S Gerber AW Ginhart O Gross S Grumann S Hermann R Jost A König R Lümann M May B Nonhoff B Reichel R Strehlow AP Stamatakis N Stuckmann A Vilbig M Lenke T Ludwig A Bode KH Schleifer, Nucleic Acids Res 2004 32 1363 1371 10.1093/nar/gkh293 14985472
32. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. E Pruesse C Quast K Knittel BM Fuchs W Ludwig J Peplies FO Glöckner, Nucl Acids Res 2007 gkm864. 17947321
33. Silva - Comprehensive Ribosomal RNA Database. http://www.arb-silva.de/
34. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. JR Cole B Chai RJ Farris Q Wang SA Kulam DM McGarrell GM Garrity JM Tiedje, Nucleic Acids Res 2005 33 294 D296 10.1093/nar/gki038 15608200
35. Ribosomal Database Project. http://rdp.cme.msu.edu
36. Basic Local Alignment Search Tool (BLAST). http://blast.ncbi.nlm.nih.gov/ Blast.cgi
37. Genotypic and phenotypic characterization of fusobacteria from Chinese and European patients with inflammatory periodontal diseases. R Gmür MA Munson WG Wade, Syst Appl Microbiol 2006 29 120 130 16464693
38. Identification of oral streptococci using PCR-based, reverese-capture, checkerboard hybridization. BJ Paster IM Bartoszyk FE Dewhirst, Meth Cell Sci 1998 20 223 231 10.1023/A:1009715710555 (Pubitemid 29241701)
39. In vitro modeling of host-parasite interactions: the 'subgingival' biofilm challenge of primary human epithelial cells. B Guggenheim R Gmür JC Galicia P Stathopoulou MR Benakanakere A Meier T Thurnheer D Kinane, BMC Microbiol 2009 9 280 10.1186/1471-2180-9-280 20043840
40. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. RI Amann BJ Binder RJ Olson SW Chisholm R Devereux DA Stahl, Appl Environ Microbiol 1990 56 1919 1925 2200342