|
QianRen Biology 2014
16SrRNA序列分析技术在口腔微生物群落中的应用
|
Abstract:
[1] | Li, Y., Saxena, D., Chen, Z., Liu, G., Abrams, W.R., Phelan, J.A., Norman, R.G., Fisch, G.S., Corby, P.M., Dewhirst, F., Paster, B.J., Kokaras, A.S. and Malamud, D. (2014) HIV infection and microbial diversity in saliva. Journal of Cli- nical Microbiology, 52, 1400-1411. |
[2] | 丁迎春, 平文祥, 孙剑秋, 周东坡 (1996) 人类口腔小生境微生物的多样性. 生物多样性, 2,103-108. |
[3] | Dewhirst, F.E., Chen, T., Izard, J., Paster, B.J., Tanner, A.C., Yu, W.H., Lakshma-nan, A. and Wade, W.G. (2010) The human oral microbiome. Journal of Bacteriology, 192, 5002-5017. |
[4] | Peer, Y.V., Chapelle, S. and Wachter, D.R. (1996) A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acids Research, 24, 3381-3391. |
[5] | Kumar, P.S., Brooker, M.R., Dowd, S.E. and Camerlengo, T. (2011) Target Region Selection Is a Critical Determinant of Community Fingerprints Generated by 16S Pyrosequencing. Plos One, 6, e20956. |
[6] | Sato, T. and Kuramitsu, H.K. (1999) Restriction fragment-length polymorphism analysis of 16S ribosomal RNA genes amplified by polymerase chain reaction for rapid identification of cultivable oral treponemes. Oral Microbiology and Immunology, 14, 117-121. |
[7] | Sato, T., Hu, J.P., Ohki, K., Yamaura, M., Washio, J. and Matsuyama, J. (2003) Identification of mutans streptococci by restriction fragment length polymorphism analysis of polymerase chain reaction-amplified 16S ribosomal RNA genes. Oral Microbiology and Immunology, 18, 323-326. |
[8] | Sanger, F. and Coulson, A.R. (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of Molecular Biology, 94, 441-448. |
[9] | Kroes, I., Lepp, P.W. and Relman, D.A. (1999) Bacterial diversity within the human subgingival crevice. Proceedings of the National Academy of Sciences of the United States of America, 96, 14547-14552. |
[10] | Suzuki, M.T. and Giovannoni, S.J. (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Applied and Environmental Microbiology, 62, 625-630. |
[11] | Nossa, C.W., Oberdorf, W.E., Yang, L., Aas, J.A., Paster, B.J., DeSantis, T.Z., Brodie, E.L., Malamud, D., Poles, M.A. and Pei, Z. (2010) Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. World Journal of Gastroenterology, 16, 4135-4144. |
[12] | Hutter, G., Schlagenhauf, U., Valenza, G., Horn, M., Burgemeister, S., Claus, H. and Vogel, U. (2003) Molecular analysis of bacteria in periodontitis: Evaluation of clone libraries, novel phylotypes and putative pathogens. Microbiology, 149, 67-75. |
[13] | Kumar, P.S., Griffen, A.L., Moeschberger, M.L. and Leys, E.J. (2005) Identification of candidate periodontal pathogens and beneficial species by quantitative 16S clonal analysis. Journal of Clinical Microbiology, 43, 3944-3955. |
[14] | 薛晶, 肖丽英, 周学东 (2010) 人体口腔微生物组研究最新进展. 华西口腔医学杂志, 1, 5-8 |
[15] | Ledder, R.G., Gilbert, P., Huws, S.A., Aarons, L., Ashley, M.P., Hull, P.S. and McBain, A.J. (2007) Molecular analysis of the subgingival microbiota in health and disease. Applied and Environmental Microbiology, 73, 516-523. |
[16] | Sakamoto, M., Huang, Y., Ohnishi, M., Umeda, M., Ishikawa, I. and Benno, Y. (2004) Changes in oral microbial profiles after periodontal treatment as determined by molecular analysis of 16S rRNA genes. Journal of Medical Microbiology, 53, 563-571. |
[17] | Balaji, K., Thenmozhi, R., Sundaravadivel, M. and Pandian, S.K. (2012) Comparison of bacterial communities in the throat swabs from healthy subjects and pharyngitis patients by terminal restriction fragment length polymorphism. Ap- plied Bio-chemistry and Biotechnology, 167, 1459-1473. |
[18] | Takeshita, T., Nakano, Y., Kumagai, T., Yasui, M., Kamio, N., Shibata, Y., Shiota, S. and Yamashita, Y. (2009) The ecological proportion of indigenous bacterial populations in saliva is correlated with oral health status. The ISME Jour- nal, 3, 65-78. |
[19] | Siqueira Jr., J.F. and R??as, I.N. (2010) The oral microbiota: General overview, taxonomy, and nucleic acid techniques. In: Seymour, G.J., Cullinan, M.P. and Heng, N.C.K., Eds., Oral Biology, Methods in Molecular Biology, Humana Press, New York, 55-69. |
[20] | Haffajee, A.D. and Socransky, S.S. (2001) Relationship of cigarette smoking to the subgingival microbiota. Journal of Clinical Periodontology, 28, 377-388. |
[21] | 汤华阳, 杜卫东, 张学军 (2007) 焦磷酸测序技术及应用. 医学分子生物学杂志, 3, 272-275. |
[22] | Ling, Z., Kong, J., Jia, P., Wei, C., Wang, Y., Pan, Z., Huang, W., Li, L., Chen, H. and Xiang, C. (2010) Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing. Mi-crobial Ecology, 60, 677-690. |
[23] | Dymock, D., Weightman, A.J., Scully, C. and Wade, W.G. (1996) Molecular analysis of microflora associated with dentoalveolar abscesses. Journal of Clinical Microbiology, 34, 537-542. |
[24] | Keijser, B.J.F., Zaura, E., Huse, S.M., van der Vossen, J.M.B.M, Schuren, F.H.J, Montijn, R.C., ten Cate, J.M. and Crielaard, W. (2008) Pyrosequencing analysis of the oral microflora of healthy adults. Journal of Dental Research, 87, 1016-1020. |
[25] | Alcaraz, L.D., Belda-Ferre, P., Cabrera-Rubio, R., Romero, H., Simón-Soro, A., Pig-natelli, M. and Mira, A. (2012) Identifying a healthy oral microbiome through metagenomics. Clinical Microbiology and Infection, 4, 54-57. |
[26] | Kianoush, N., Adler, C.J., Nguyen, K.A., Browne, G.V., Simonian, M. and Hunter, N. (2014) Bacterial profile of dentine caries and the impact of pH on bacterial population diversity. PLoS ONE, 9, e92940. |
[27] | Langfeldt, D., Neulinger, S.C., Heuer, W., Staufenbiel, I., Künzel, S., Baines, J.F., Eberhard, J. and Schmitz, R.A. (2014) Composition of microbial oral biofilms during maturation in young healthy adults. PLoS ONE, 9, e87449. |
[28] | Ahn, J., Yang, L., Paster, B.J., Ganly, I., Morris, L., Pei, Z. and Hayes, R.B. (2011) Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison. PLoS ONE, 6, e22788. |
[29] | Rasiah, I.A., Wong, L., Anderson, S.A. and Sissons, C.H. (2005) Variation in bacterial DGGE patterns from human saliva: Over time, between individuals and in corresponding dental plaque microcosms. Archives of Oral Biology, 50, 779-787. |
[30] | Nasidze, I., Li, J., Quinque, D., Tang, K. and Stoneking, M. (2009) Global diversity in the human salivary microbiome. Genome Research, 19, 636-643 |
[31] | Gusberti, F.A., Mombelli, A., Lang, N.P. and Minder, C.E. (1990) Changes in subgingival microbiota during puberty: A 4-year longitudinal study. Journal of Clinical Periodontology, 17, 685-692. |
[32] | Takahashi, N. and Nyvad, B. (2011) The role of bacteria in the caries process: Ecological perspectives. Journal of Dental Research, 90, 294-303 |
[33] | Munson, M.A., Banerjee, A., Watson, T.F. and Wade, W.G. (2004) Molecular analysis of the micro?ora associated with dental caries. Journal of Clinical Microbiology, 42, 3023-3029. |
[34] | Kleinberg, I. (2002) A mixed-bacteria ecological approach to understanding the role of the oral bacteria in dental caries causation: An alternative to Streptococcus mutans and the specific-plaque hypothesis. Critical Reviews in Oral Biology & Medicine, 13, 108-125. |
[35] | Gross, E.L., Leys, E.J., Gasparovich, S.R., Firestone, N.D., Schwartzbaum, J.A., Janies, D.A., Asnani, K. and Griffen, A.L. (2010) Bacterial 16S sequence analysis of severe caries in young permanent teeth. Journal of Clinical Microbiology, 48, 4121-4128. |
[36] | Kaur, R., Gilbert, S.C., Sheehy, E.C. and Beighton, D. (2013) Salivary levels of bi?dobacteria in caries-free and caries-active children. International Journal of Paediatric Dentistry, 23, 32-38. |
[37] | Downes, J., Mantzourani, M., Beighton, D., Hooper, S., Wilson, M.J., Nicholson, A. and Wade, W.G. (2011) Scardovia wiggsiae sp. Nov., isolated from the human oral cavity and clinical material, and emended descriptions of the genus Scardovia and Scardovia inopinata. International Journal of Systematic and Evolutionary Microbiology, 61, 25-29. |
[38] | Tanner, A.C.R., Kent Jr., R.L., Lif Holgerson, P., Hughes, C.V., Loo, C.Y., Kanasi, E., Chalmers, N.I. and Johansson, I. (2011) Microbiota of severe early child hood caries before and after therapy. Journal of Dental Research, 90, 1298- 1305. |
[39] | Huang, S., Yang, F., Zeng, X., Chen, J., Li, R., Wen, T., Li, C., Wei, W., Liu, J., Chen, L., Davis, C. and Xu, J. (2011) Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis. BMC Oral Health, 11, 33. |
[40] | Nyvad, B. and Kilian, M. (1987) Microbiology of the early colonization of human enamel and root surfaces in vivo. Journal of Dental Research, 95, 369-380. |
[41] | Zijnge, V., van Leeuwen, M.B., Degener, J.E., Abbas, F., Thurnheer, T., Gmür, R. and Harmsen, H.J. (2010) Oral bio?lm architecture on natural teeth. PLoS ONE, 5, e9321. |
[42] | Lovegrove, J.M. (2004) Dental plaque revisited: Bacteria associated with periodontal disease. Journal of the New Zealand Society of Periodontology, 87, 7-21. |
[43] | Van Dyke, T.E. and Sheilesh, D. (2005) Risk factors for periodontitis. Journal of the New Zealand Society of Periodontology, 7, 3-7. |
[44] | Haffajee, A.D., Socransky, S.S., Patel, M.R. and Song, X. (2008) Microbial complexes in subgingival plaque. Oral Microbiology and Immunology, 25, 134-144. |
[45] | Kumar, P.S., Griffen, A.L., Barton, J.A., Paster, B.J., Moeschberger, M.L. and Leys, E.J. (2003) New bacterial species associated with chronic periodontitis. Journal of Dental Research, 82, 338-344. |
[46] | Wang, J., Qi, J., Zhao, H., He, S., Zhang, Y., Wei, S. and Zhao, F. (2013) Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Scientific Reports, 3, 1843. |