Comparison of bacterial culture and 16S rRNA community profiling by clonal analysis and pyrosequencing for the characterization of the dentine caries-associated microbiome

Frontiers in Cellular and Infection Microbiology

Volumn 4, Issue NOV, 2014, Pages

  Schulze Schweifing, Kathrin ^a   Banerjee, Avijit ^a   Wade, William G ^b  

^a KING'S COLLEGE LONDON   (United Kingdom)

^b QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Caries; Caries infected dentine; Oral microbiome

Indexed keywords

PRIMER RNA; RNA 16S;

ACTINOBACTERIA; ADULT; ARTICLE; BACTERIUM CULTURE; BACTERIUM EXAMINATION; BACTEROIDETES; CLINICAL ARTICLE; CLONAL ANALYSIS; COMPARATIVE STUDY; CULTURE MEDIUM; DENTAL CARIES; DENTIN; DNA EXTRACTION; FEMALE; FIRMICUTES; FUSOBACTERIA; GENE EXPRESSION PROFILING; GENE SEQUENCE; HUMAN; LACTOBACILLUS; MALE; MICROBIAL COMMUNITY; MICROBIOME; NONHUMAN; POLYMERASE CHAIN REACTION; PREVOTELLA; PROTEOBACTERIA; PYROSEQUENCING; SELENOMONAS; SPIROCHETE; STREPTOCOCCUS; CLASSIFICATION; DNA SEQUENCE; GENETICS; METAGENOME; MICROBIOLOGY; MICROFLORA; PATHOLOGY; PHYLOGENY; YOUNG ADULT;

ADULT; DENTAL CARIES; DENTIN; FEMALE; HUMANS; MALE; METAGENOME; MICROBIOTA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; STREPTOCOCCUS; YOUNG ADULT;

EID: 84915817893     PISSN: None     EISSN: 22352988     Source Type: Journal    
DOI: 10.3389/fcimb.2014.00164     Document Type: Article

References (38)

1. Aas, J. A., Griffen, A. L., Dardis, S. R., Lee, A. M., Olsen, I., Dewhirst, F. E., et al. (2008). Bacteria of dental caries in primary and permanent teeth in children and young adults. J. Clin. Microbiol. 46, 1407-1417. doi: 10.1128/JCM.01410-07
2. Belda-Ferre, P., Alcaraz, L. D., Cabrera-Rubio, R., Romero, H., Simon-Soro, A., Pignatelli, M., et al. (2012). The oral metagenome in health and disease. ISME J. 6, 46-56. doi: 10.1038/ismej.2011.85
3. Bru, D., Martin-Laurent, F., and Philippot, L. (2008). Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example. Appl. Environ. Microbiol. 74, 1660-1663. doi: 10.1128/AEM.02403-07
4. Byun, R., Nadkarni, M. A., Chhour, K. L., Martin, F. E., Jacques, N. A., and Hunter, N. (2004). Quantitative analysis of diverse Lactobacillus species present in advanced dental caries. J. Clin. Microbiol. 42, 3128-3136. doi: 10.1128/JCM.42.7.3128-3136.2004
5. Chen, T., Yu, W. H., Izard, J., Baranova, O. V., Lakshmanan, A., and Dewhirst, F. E. (2010). The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database 2010:baq013. doi: 10.1093/database/baq013
6. Chhour, K. L., Nadkarni, M. A., Byun, R., Martin, F. E., Jacques, N. A., and Hunter, N. (2005). Molecular analysis of microbial diversity in advanced caries. J. Clin. Microbiol. 43, 843-849. doi: 10.1128/JCM.43.2.843-849.2005
7. Clarke, J. K. (1924). On the bacterial factor in the aetiology of dental caries. Br. J. Exp. Pathol. 5, 141-147.
8. de Lillo, A., Ashley, F. P., Palmer, R. M., Munson, M. A., Kyriacou, L., Weightman, A. J., et al. (2006). Novel subgingival bacterial phylotypes detected using multiple universal polymerase chain reaction primer sets. Oral Microbiol. Immunol. 21, 61-68. doi: 10.1111/j.1399-302X.2005.00255.x
9. Dewhirst, F. E., Chen, T., Izard, J., Paster, B. J., Tanner, A. C., Yu, W. H., et al. (2010). The human oral microbiome. J. Bacteriol. 192, 5002-5017. doi: 10.1128/JB.00542-10
10. Diaz, P. I., Dupuy, A. K., Abusleme, L., Reese, B., Obergfell, C., Choquette, L., et al. (2012). Using high throughput sequencing to explore the biodiversity in oral bacterial communities. Mol. Oral Microbiol. 27, 182-201. doi: 10.1111/j.2041-1014.2012.00642.x
11. Frank, J. A., Reich, C. I., Sharma, S., Weisbaum, J. S., Wilson, B. A., and Olsen, G. J. (2008). Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl. Environ. Microbiol. 74, 2461-2470. doi: 10.1128/AEM.02272-07
12. Gross, E. L., Leys, E. J., Gasparovich, S. R., Firestone, N. D., Schwartzbaum, J. A., Janies, D. A., et al. (2010). Bacterial 16S sequence analysis of severe caries in young permanent teeth. J. Clin. Microbiol. 48, 4121-4128. doi: 10.1128/JCM.01232-10
13. Kanasi, E., Dewhirst, F. E., Chalmers, N. I., Kent, R. Jr., Moore, A., Hughes, C. V., et al. (2010). Clonal analysis of the microbiota of severe early childhood caries. Caries Res. 44, 485-497. doi: 10.1159/000320158
14. Keijser, B. J., Zaura, E., Huse, S. M., van der Vossen, J. M., Schuren, F. H., Montijn, R. C., et al. (2008). Pyrosequencing analysis of the oral microflora of healthy adults. J. Dent. Res. 87, 1016-1020. doi: 10.1177/154405910808701104
15. Lane, D. J. (1991). "16S/23S rRNA sequencing," in Nucleic Acid Techniques In Bacterial Systematics, eds E. Stackebrandt and M. Goodfellow (Chichester: John Wiley & Sons), 115-175.
16. Lima, K. C., Coelho, L. T., Pinheiro, I. V., Rocas, I. N., and Siqueira, J. F. Jr. (2011). Microbiota of dentinal caries as assessed by reverse-capture checkerboard analysis. Caries Res. 45, 21-30. doi: 10.1159/000322299
17. Lin, S. Y., Shen, F. T., and Young, C. C. (2011). Rapid detection and identification of the free-living nitrogen fixing genus Azospirillum by 16S rRNA-gene-targeted genus-specific primers. Antonie van Leeuwenhoek 99, 837-844. doi: 10.1007/s10482-011-9558-1
18. Loesche, W. J., Rowan, J., Straffon, L. H., and Loos, P. J. (1975). Association of Streptococcus mutants with human dental decay. Infect. Immun. 11, 1252-1260.
19. Marchesi, J. R., Sato, T., Weightman, A. J., Martin, T. A., Fry, J. C., Hiom, S. J., et al. (1998). Design, and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl. Environ. Microbiol. 64, 795-799.
20. Marsh, P. D. (2003). Are dental diseases examples of ecological catastrophes? Microbiology 149(Pt 2), 279-294. doi: 10.1099/mic.0.26082-0
21. Marsh, P. D., Featherstone, A., McKee, A. S., Hallsworth, A. S., Robinson, C., Weatherell, J. A., et al. (1989). A microbiological study of early caries of approximal surfaces in schoolchildren. J. Dent. Res. 68, 1151-1154. doi: 10.1177/00220345890680070301
22. Munson, M. A., Banerjee, A., Watson, T. F., and Wade, W. G. (2004). Molecular analysis of the microflora associated with dental caries. J. Clin. Microbiol. 42, 3023-3029. doi: 10.1128/JCM.42.7.3023-3029.2004
23. Munson, M. A., Pitt Ford, T., Chong, B., Weightman, A. J., and Wade, W. G. (2002). Molecular and cultural analysis of the microflora associated with endodontic infections. J. Dent. Res. 81, 761-766. doi: 10.1177/154405910208101108
24. Nadkarni, M. A., Caldon, C. E., Chhour, K. L., Fisher, I. P., Martin, F. E., Jacques, N. A., et al. (2004). Carious dentine provides a habitat for a complex array of novel Prevotella-like bacteria. J. Clin. Microbiol. 42, 5238-5244. doi: 10.1128/JCM.42.11.5238-5244.2004
25. Palatinszky, M., Nikolausz, M., Svab, D., and Marialigeti, K. (2011). Preferential ligation during TA-cloning of multitemplate PCR products-a factor causing bias in microbial community structure analysis. J. Microbiol. Methods 85, 131-136. doi: 10.1016/j.mimet.2011.02.007
26. Paster, B. J., Boches, S. K., Galvin, J. L., Ericson, R. E., Lau, C. N., Levanos, V. A., et al. (2001). Bacterial diversity in human subgingival plaque. J. Bacteriol. 183, 3770-3783. doi: 10.1128/JB.183.12.3770-3783.2001
27. Paster, B. J., Olsen, I., Aas, J. A., and Dewhirst, F. E. (2006). The breadth of bacterial diversity in the human periodontal pocket and other oral sites. Periodontol 2000 42, 80-87. doi: 10.1111/j.1600-0757.2006.00174.x
28. Pedros-Alio, C. (2012). The rare bacterial biosphere. Ann. Rev. Mar. Sci. 4, 449-466. doi: 10.1146/annurev-marine-120710-100948
29. Reeder, J., and Knight, R. (2009). The "rare biosphere": a reality check. Nat. Methods 6, 636-637. doi: 10.1038/nmeth0909-636
30. Schloss, P. D., and Westcott, S. L. (2011). Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl. Environ. Microbiol. 77, 3219-3226. doi: 10.1128/AEM.02810-10
31. Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., et al. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541. doi: 10.1128/AEM.01541-09
32. Takahashi, N., and Nyvad, B. (2011). The role of bacteria in the caries process: ecological perspectives. J. Dent. Res. 90, 294-303. doi: 10.1177/0022034510379602
33. Tanner, A. C., Mathney, J. M., Kent, R. L., Chalmers, N. I., Hughes, C. V., Loo, C. Y., et al. (2011). Cultivable anaerobic microbiota of severe early childhood caries. J. Clin. Microbiol. 49, 1464-1474. doi: 10.1128/JCM.02427-10
34. Taylor, D. L., Herriott, I. C., Long, J., and O'Neill, K. (2007). TOPO TA is A-OK: a test of phylogenetic bias in fungal environmental clone library construction. Environ. Microbiol. 9, 1329-1334. doi: 10.1111/j.1462-2920.2007.01253.x
35. Vartoukian, S. R., Palmer, R. M., and Wade, W. G. (2009). Diversity and morphology of members of the phylum "synergistetes" in periodontal health and disease. Appl. Environ. Microbiol. 75, 3777-3786. doi: 10.1128/AEM.02763-08
36. Wang, Y., Hammes, F., Boon, N., Chami, M., and Egli, T. (2009). Isolation and characterization of low nucleic acid (LNA)-content bacteria. ISME J. 3, 889-902. doi: 10.1038/ismej.2009.46
37. Wu, J. H., Hong, P. Y., and Liu, W. T. (2009). Quantitative effects of position and type of single mismatch on single base primer extension. J. Microbiol. Methods 77, 267-275. doi: 10.1016/j.mimet.2009.03.001
38. Xie, Q., Hong, K., and Goodfellow, M. (2011). Genus-specific primers targeting the 16S rRNA gene for PCR detection of members of the genus Verrucosispora. Antonie Van Leeuwenhoek 100, 117-128. doi: 10.1007/s10482-011-9571-4