Pyrosequencing of supra- and subgingival biofilms from inflamed peri-implant and periodontal sites

BMC Oral Health

Meike Stiesch⁴  Jörg Eberhard¹  Sascha Nico Stumpp⁴  Andreas Winkel⁴  Markus Schilhabel³  Ralph Scherer⁵  Ingmar Staufenbiel²  Simone Schaumann⁴ 

[1] Peri-implant and Oral Infections, Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany;Department of Conservative Dentistry, Periodontology and Preventive Dentistry, Hannover Medical School, Hannover, Germany;Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany;Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany;Institute for Biometry, Hannover Medical School, Hannover, Germany

关键词: Microbiology;    Biofilm;    Subgingival plaque;    Supragingival plaque;    Diseased periodontal tissues;    Diseased peri-implant tissues;    16S rRNA sequencing;    Deep-sequencing;   

Others  :  1090685
DOI  :  10.1186/1472-6831-14-157

 received in 2014-08-28, accepted in 2014-12-15,  发布年份 2014

【 摘 要 】

Background

To investigate the microbial composition of biofilms at inflamed peri-implant and periodontal tissues in the same subject, using 16S rRNA sequencing.

Methods

Supra- and submucosal, and supra- and subgingival plaque samples were collected from 7 subjects suffering from diseased peri-implant and periodontal tissues. Bacterial DNA was isolated and 16S rRNA genes were amplified, sequenced and aligned for the identification of bacterial genera.

Results

43734 chimera-depleted, denoised sequences were identified, corresponding to 1 phylum, 8 classes, 10 orders, 44 families and 150 genera. The most abundant families or genera found in supramucosal or supragingival plaque were Streptoccocaceae, Rothia and Porphyromonas. In submucosal plaque, the most abundant family or genera found were Rothia, Streptococcaceae and Porphyromonas on implants. The most abundant subgingival bacteria on teeth were Prevotella, Streptococcaceae, and TG5. The number of sequences found for the genera Tannerella and Aggregatibacter on implants differed significantly between supra- and submucosal locations before multiple testing. The analyses demonstrated no significant differences between microbiomes on implants and teeth in supra- or submucosal and supra- or subgingival biofilms.

Conclusion

Diseased peri-implant and periodontal tissues in the same subject share similiar bacterial genera and based on the analysis of taxa on a genus level biofilm compositions may not account for the potentially distinct pathologies at implants or teeth.

【 授权许可】

   
2014 Schaumann et al.; licensee BioMed Central.

【 图 表 】

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【 参考文献 】

• [1]Mombelli A, Muller N, Cionca N: The epidemiology of peri-implantitis. Clin Oral Implants Res 2012, 23(Suppl 6):67-76.
• [2]Heitz-Mayfield LJ: Peri-implant diseases: diagnosis and risk indicators. J Clin Periodontol 2008, 35(8 Suppl):292-304.
• [3]Shibli JA, Melo L, Ferrari DS, Figueiredo LC, Faveri M, Feres M: Composition of supra- and subgingival biofilm of subjects with healthy and diseased implants. Clin Oral Implants Res 2008, 19(10):975-982.
• [4]Persson GR, Samuelsson E, Lindahl C, Renvert S: Mechanical non-surgical treatment of peri-implantitis: a single-blinded randomized longitudinal clinical study. II. Microbiological results. J Clin Periodontol 2010, 37(6):563-573.
• [5]Maximo MB, de Mendonca AC, Renata Santos V, Figueiredo LC, Feres M, Duarte PM: Short-term clinical and microbiological evaluations of peri-implant diseases before and after mechanical anti-infective therapies. Clin Oral Implants Res 2009, 20(1):99-108.
• [6]Salcetti JM, Moriarty JD, Cooper LF, Smith FW, Collins JG, Socransky SS, Offenbacher S: The clinical, microbial, and host response characteristics of the failing implant. Int J Oral Maxillofac Implants 1997, 12(1):32-42.
• [7]Kumar PS, Mason MR, Brooker MR, O'Brien K: Pyrosequencing reveals unique microbial signatures associated with healthy and failing dental implants. J Clin Periodontol 2012, 39(5):425-433.
• [8]Koyanagi T, Sakamoto M, Takeuchi Y, Maruyama N, Ohkuma M, Izumi Y: Comprehensive microbiological findings in peri-implantitis and periodontitis. J Clin Periodontol 2013, 40(3):218-226.
• [9]Dabdoub SM, Tsigarida AA, Kumar PS: Patient-specific analysis of periodontal and peri-implant microbiomes. J Dent Res 2013, 92(12 Suppl):168S-175S.
• [10]Hellstrom MK, Ramberg P, Krok L, Lindhe J: The effect of supragingival plaque control on the subgingival microflora in human periodontitis. J Clin Periodontol 1996, 23(10):934-940.
• [11]Socransky SS, Haffajee AD: Dental biofilms: difficult therapeutic targets. Periodontol 2000 2002, 28:12-55.
• [12]Tezal M, Scannapieco FA, Wactawski-Wende J, Grossi SG, Genco RJ: Supragingival plaque may modify the effects of subgingival bacteria on attachment loss. J Periodontol 2006, 77(5):808-813.
• [13]Teughels W, Van Assche N, Sliepen I, Quirynen M: Effect of material characteristics and/or surface topography on biofilm development. Clin Oral Implants Res 2006, 17(Suppl 2):68-81.
• [14]Heitz-Mayfield LJ, Lang NP: Comparative biology of chronic and aggressive periodontitis vs. peri-implantitis. Periodontol 2000 2010, 53:167-181.
• [15]Lange DE, Plagmann H-C, Eenboom A, Promesberger A: Klinische Bewertungsverfahren zur Objektivierung der Mundhygiene. Dtsch zahnärztl Z 1977, 32:44-47.
• [16]Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R: QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010, 7(5):335-336.
• [17]Reeder J, Knight R: Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods 2010, 7(9):668-669.
• [18]R Core Team: R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2013. http://www.R-project.org webcite
• [19]Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80. BioMed Central Full Text
• [20]McMurdie PJ, Holmes S: phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 2013, 8(4):e61217.
• [21]Robinson MD, McCarthy DJ, Smyth GK: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26(1):139-140.
• [22]Shannon CE: The mathematical theory of communication. MD Comput 1997 1963, 14(4):306-317.
• [23]Bizzarro S, Loos BG, Laine ML, Crielaard W, Zaura E: Subgingival microbiome in smokers and non-smokers in periodontitis: an exploratory study using traditional targeted techniques and a next-generation sequencing. J Clin Periodontol 2013, 40(5):483-492.
• [24]Hu YJ, Wang Q, Jiang YT, Ma R, Xia WW, Tang ZS, Liu Z, Liang JP, Huang ZW: Characterization of oral bacterial diversity of irradiated patients by high-throughput sequencing. Int J Oral Sci 2013, 5(1):21-25.
• [25]Tanner AC, Haffer C, Bratthall GT, Visconti RA, Socransky SS: A study of the bacteria associated with advancing periodontitis in man. J Clin Periodontol 1979, 6(5):278-307.
• [26]Lesher RJ, Gerencser VF, Morrison DJ: Presence of Rothia dentocariosa strain 477 serotype 2 in gingiva of patients with inflammatory periodontal disease. J Dent Res 1977, 56(2):189.
• [27]Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J: Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol 2012, 13(6):R42. BioMed Central Full Text
• [28]Kistler JO, Booth V, Bradshaw DJ, Wade WG: Bacterial community development in experimental gingivitis. PLoS One 2013, 8(8):e71227.
• [29]Abusleme L, Dupuy AK, Dutzan N, Silva N, Burleson JA, Strausbaugh LD, Gamonal J, Diaz PI: The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. ISME J 2013, 7(5):1016-1025.
• [30]da Silva ES, Feres M, Figueiredo LC, Shibli JA, Ramiro FS, Faveri M: Microbiological diversity of peri-implantitis biofilm by Sanger sequencing. Clin Oral Implants Res 2014, 25(10):1192-1199.
• [31]Shakoor S, Fasih N, Jabeen K, Jamil B: Rothia dentocariosa endocarditis with mitral valve prolapse: case report and brief review. Infection 2011, 39(2):177-179.
• [32]Trivedi MN, Malhotra P: Rothia prosthetic knee joint infection. J Microbiol Immunol Infect 2013, 25:243-245.
• [33]Kataoka H, Taniguchi M, Fukamachi H, Arimoto T, Morisaki H, Kuwata H: Rothia dentocariosa induces TNF-alpha production in a TLR2-dependent manner. Pathog Dis 2014, 71(1):65-68.
• [34]Chen T, Yu WH, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE: The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford) 2010, 2010:baq013.
• [35]Inbakandan D, Murthy PS, Venkatesan R, Khan SA: 16S rDNA sequence analysis of culturable marine biofilm forming bacteria from a ship's hull. Biofouling 2010, 26(8):893-899.
• [36]Wen W, Wang S, Zhou X, Fang B: Central carbon metabolism in marine bacteria examined with a simplified assay for dehydrogenases. Appl Biochem Biotechnol 2013, 170(3):473-482.
• [37]Yang J, Wang C, Wu J, Liu L, Zhang G, Feng J: Characterization of a multi-resistant mosaic plasmid from a fish farm sediment Exiguobacterium sp. isolate reveals aggregation of functional clinically-associated antibiotic resistance genes. Appl Environ Microbiol 2014, 80(4):1482-1488.
• [38]Vishnivetskaya TA, Kathariou S, Tiedje JM: The Exiguobacterium genus: biodiversity and biogeography. Extremophiles 2009, 13(3):541-555.
• [39]van der Horst J, Buijs MJ, Laine ML, Wismeijer D, Loos BG, Crielaard W, Zaura E: Sterile paper points as a bacterial DNA-contamination source in microbiome profiles of clinical samples. J Dent 2013, 41(12):1297-1301.
• [40]Sumida S, Ishihara K, Kishi M, Okuda K: Transmission of periodontal disease-associated bacteria from teeth to osseointegrated implant regions. Int J Oral Maxillofac Implants 2002, 17(5):696-702.
• [41]Quirynen M, Papaioannou W, van Steenberghe D: Intraoral transmission and the colonization of oral hard surfaces. J Periodontol 1996, 67(10):986-993.
• [42]Quirynen M, Vogels R, Peeters W, van Steenberghe D, Naert I, Haffajee A: Dynamics of initial subgingival colonization of 'pristine' peri-implant pockets. Clin Oral Implants Res 2006, 17(1):25-37.
• [43]Ximenez-Fyvie LA, Haffajee AD, Socransky SS: Microbial composition of supra- and subgingival plaque in subjects with adult periodontitis. J Clin Periodontol 2000, 27(10):722-732.
• [44]Cortelli SC, Cortelli JR, Romeiro RL, Costa FO, Aquino DR, Orzechowski PR, Araujo VC, Duarte PM: Frequency of periodontal pathogens in equivalent peri-implant and periodontal clinical statuses. Arch Oral Biol 2013, 58(1):67-74.