Subgingival microbiota in individuals with severe chronic periodontitis

Journal of Microbiology, Immunology and Infection

Volumn 51, Issue 2, 2018, Pages 226-234

  Tsai, Chi Ying ^a   Tang, Chuan Yi ^b,c   Tan, Te Sheng ^b   Chen, Kuan Hsueh ^c   Liao, Ki Hok ^b   Liou, Ming Li ^d  

^a CHANG GUNG MEMORIAL HOSPITAL   (Taiwan)

^b NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^c PROVIDENCE UNIVERSITY   (Taiwan)

^d YUANPEI UNIVERSITY   (Taiwan)

Author keywords

16S rRNA metagenomics; severe chronic periodontitis

Indexed keywords

RNA 16S;

ACTINOMYCES; AGGREGATIBACTER; ARTICLE; BACTERIUM; CAPNOCYTOPHAGA; CHRONIC PERIODONTITIS; CLINICAL ARTICLE; CONTROLLED STUDY; FILIFACTOR; HAEMOPHILUS; HUMAN; LAUTROPIA; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MOUTH FLORA; NONHUMAN; PALUDIBACTER; PARVIMONAS; PEPTOSTREPTOCOCCUS; POLYMERASE CHAIN REACTION; PORPHYROMONAS; PREVOTELLA; QUANTITATIVE ANALYSIS; STREPTOCOCCUS; STREPTOCOCCUS ORALIS; TAIWANESE; TANNERELLA; TANNERELLA FORSYTHIA; TREPONEMA; BIODIVERSITY; CLASSIFICATION; DNA SEQUENCE; GENETICS; GINGIVA; ISOLATION AND PURIFICATION; MICROBIOLOGY; MICROFLORA; NUCLEOTIDE SEQUENCE; REAL TIME POLYMERASE CHAIN REACTION; TAIWAN;

BACTERIA; BASE SEQUENCE; BIODIVERSITY; CHRONIC PERIODONTITIS; GINGIVA; HUMANS; MICROBIOTA; REAL-TIME POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; TAIWAN;

EID: 84976491196     PISSN: 16841182     EISSN: 19959133     Source Type: Journal    
DOI: 10.1016/j.jmii.2016.04.007     Document Type: Article

References (33)

1. Armitage, G.C., Development of a classification system for periodontal diseases and conditions. Ann Periodontol 4 (1999), 1–6.
2. Pihlstrom, B.L., Michalowicz, B.S., Johnson, N.W., Periodontal diseases. Lancet 366 (2005), 1809–1820.
3. Humphrey, L.L., Fu, R., Buckley, D.I., Freeman, M., Helfand, M., Periodontal disease and coronary heart disease incidence: a systematic review and meta-analysis. J Gen Intern Med 23 (2008), 2079–2086.
4. Socransky, S.S., Haffajee, A.D., Cugini, M.A., Smith, C., Kent, R.L. Jr., Microbial complexes in subgingival plaque. J Clin Periodontol 25 (1998), 134–144.
5. Slots, J., Genco, R.J., Black-pigmented Bacteroides species, Capnocytophaga species, and Actinobacillus actinomycetemcomitans in human periodontal disease: virulence factors in colonization, survival, and tissue destruction. J Dent Res 63 (1984), 412–421.
6. Kolenbrander, P.E., Andersen, R.N., Moore, L.V., Coaggregation of Fusobacterium nucleatum, Selenomonas flueggei, Selenomonas infelix, Selenomonas noxia, and Selenomonas sputigena with strains from 11 genera of oral bacteria. Infect Immun 57 (1989), 3194–3203.
7. Paster, B.J., Olsen, I., Aas, J.A., Dewhirst, F.E., The breadth of bacterial diversity in the human periodontal pocket and other oral sites. Periodontol 2000 42 (2006), 80–87.
8. Tringe, S.G., Hugenholtz, P., A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11 (2008), 442–446.
9. Liu, B., Faller, L.L., Klitgord, N., Mazumdar, V., Ghodsi, M., Sommer, D.D., et al. Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One, 7, 2012, e37919, 10.1371/journal.pone.0037919.
10. Wang, J., Qi, J., Zhao, H., He, S., Zhang, Y., Wei, S., et al. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep, 3, 2013, 1843.
11. Laksmana, T., Kittichotirat, W., Huang, Y., Chen, W., Jorgensen, M., Bumgarner, R., et al. Metagenomic analysis of subgingival microbiota following non-surgical periodontal therapy: a pilot study. Open Dent J 6 (2012), 255–261.
12. Chen, H., Liu, Y., Zhang, M., Wang, G., Qi, Z., Bridgewater, L., et al. A Filifactor alocis-centered co-occurrence group associates with periodontitis across different oral habitats. Sci Rep, 5, 2015, 9053.
13. Darveau, R.P., Periodontitis: a polymicrobial disruption of host homeostasis. Nat Rev Microbiol 8 (2010), 481–490.
14. Van Dyke, T.E., Sheilesh, D., Risk factors for periodontitis. J Int Acad Periodontol 7 (2005), 3–7.
15. Dye, B.A., Global periodontal disease epidemiology. Periodontol 2000 58 (2012), 10–25.
16. Cai, L., Ye, L., Tong, A.H., Lok, S., Zhang, T., Biased diversity metrics revealed by bacterial 16S pyrotags derived from different primer sets. PLoS One, 8, 2013, e53649, 10.1371/journal.pone.0053649.
17. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7 (2010), 335–336.
18. Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., Knight, R., UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27 (2011), 2194–2200.
19. Edgar, R.C., UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10 (2013), 996–998.
20. McDonald, D., Price, M.N., Goodrich, J., Nawrocki, E.P., DeSantis, T.Z., Probst, A., et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6 (2012), 610–618.
21. Chen, T., Yu, W.H., Izard, J., Baranova, O.V., Lakshmanan, A., Dewhirst, F.E., The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford), 2010 http://dx.doi.org/10.1093/database/baq013.
22. Shi, B., Chang, M., Martin, J., Mitreva, M., Lux, R., Klokkevold, P., et al. Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis. MBio 6 (2015), e01926–01914, 10.1128/mBio.01926-14.
23. Staley, J.T., The bacterial species dilemma and the genomic-phylogenetic species concept. Philos Trans R Soc Lond B Biol Sci 361 (2006), 1899–1909.
24. Acinas, S.G., Marcelino, L.A., Klepac-Ceraj, V., Polz, M.F., Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186 (2004), 2629–2635.
25. Crosby, L.D., Criddle, C.S., Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34 (2003), 790–794 796, 798 passim.
26. Garza, D.R., Dutilh, B.E., From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems. Cell Mol Life Sci 72 (2015), 4287–4308.
27. Griffen, A.L., Beall, C.J., Campbell, J.H., Firestone, N.D., Kumar, P.S., Yang, Z.K., et al. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. ISME J 6 (2012), 1176–1185.
28. Abusleme, L., Dupuy, A.K., Dutzan, N., Silva, N., Burleson, J.A., Strausbaugh, L.D., et al. The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. ISME J 7 (2013), 1016–1025.
29. Nasidze, I., Li, J., Quinque, D., Tang, K., Stoneking, M., Global diversity in the human salivary microbiome. Genome Res 19 (2009), 636–643.
30. von Wintzingerode, F., Gobel, U.B., Stackebrandt, E., Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21 (1997), 213–229.
31. Kumar, P.S., Griffen, A.L., Moeschberger, M.L., Leys, E.J., Identification of candidate periodontal pathogens and beneficial species by quantitative 16S clonal analysis. J Clin Microbiol 43 (2005), 3944–3955.
32. Wade, W.G., Has the use of molecular methods for the characterization of the human oral microbiome changed our understanding of the role of bacteria in the pathogenesis of periodontal disease?. J Clin Periodontol 38:Suppl. 11 (2011), 7–16.
33. Maruyama, N., Maruyama, F., Takeuchi, Y., Aikawa, C., Izumi, Y., Nakagawa, I., Intraindividual variation in core microbiota in peri-implantitis and periodontitis. Sci Rep, 4, 2014, 6602.