Bacterial community shift in treated periodontitis patients revealed by Ion Torrent 16S rRNA gene amplicon sequencing

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Jünemann, Sebastian ^a,b   Prior, Karola ^a   Szczepanowski, Rafael ^a   Harks, Inga ^a   Ehmke, Benjamin ^a   Goesmann, Alexander ^b   Stoye, Jens ^b   Harmsen, Dag ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMOXICILLIN; ANTIBIOTIC AGENT; METRONIDAZOLE; RNA 16S;

AMPLICON; ARTICLE; BACTERIAL VIRULENCE; CASE REPORT; CONTROLLED STUDY; GENE SEQUENCE; HUMAN; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; PERIODONTAL DISEASE; POPULATION ABUNDANCE; PORPHYROMONAS; PREVENTIVE DENTISTRY; PYROSEQUENCING; SPECIES RICHNESS; TANNERELLA; TAXONOMIC RANK; TREPONEMA;

ANTI-BACTERIAL AGENTS; DNA, BACTERIAL; DNA, RIBOSOMAL; FEMALE; GRAM-NEGATIVE BACTERIA; GRAM-NEGATIVE BACTERIAL INFECTIONS; HUMANS; MALE; METAGENOME; PERIODONTITIS; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); FILIFACTOR; FORSYTHIA; OTUS; PORPHYROMONAS; PORPHYROMONAS GINGIVALIS; TANNERELLA; TREPONEMA;

EID: 84864754044     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0041606     Document Type: Article

References (42)

1. Pihlstrom BL, Michalowicz BS, Johnson NW, (2005) Periodontal diseases. Lancet 366: 1809-1820.
2. Paster BJ, Olsen I, Aas JA, Dewhirst FE, (2006) The breadth of bacterial diversity in the human periodontal pocket and other oral sites. Periodontol 2000 42: 80-87.
3. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner ACR, et al. (2010) The human oral microbiome. J Bacteriol 192: 5002-5017.
4. Keijser BJF, Zaura E, Huse SM, van der Vossen JMBM, Schuren FHJ, et al. (2008) Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res 87: 1016-1020.
5. Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, et al. (2009) Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Methods 79: 266-271.
6. Herrera D, Sanz M, Jepsen S, Needleman I, Roldán S, (2002) A systematic review on the effect of systemic antimicrobials as an adjunct to scaling and root planing in periodontitis patients. J Clin Periodontol 29 Suppl 3: 136-59; discussion 160-2.
7. Haffajee AD, Socransky SS, Gunsolley JC, (2003) Systemic anti-infective periodontal therapy: a systematic review. Ann Periodontol 8: 115-181.
8. Huber JA, Welch DBM, Morrison HG, Huse SM, Neal PR, et al. (2007) Microbial population structures in the deep marine biosphere. Science 318: 97-100.
9. Sambrook J, Russell DW, (2001) Molecular Cloning: A Laboratory Manual, 3rd edition. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
10. Linke B, Giegerich R, Goesmann A, (2011) Conveyor: a workflow engine for bioinformatic analyses. Bioinformatics 27: 903-911.
11. Martin M, (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal 17.1: 10-12.
12. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R, (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
13. Huse SM, Welch DM, Morrison HG, Sogin ML, (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12: 1889-1898.
14. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
15. Sun Y, Cai Y, Liu L, Yu F, Farrell ML, et al. (2009) ESPRIT: estimating species richness using large collections of 16s rRNA pyrosequences. Nucleic Acids Res 37: e76.
16. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P, (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123.
17. Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, et al. (2010) 454 pyrosequencing and sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytol 188: 291-301.
18. Chao A, (1984) Non-parametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 11: 265-270.
19. Magurran AE, (2003) Measuring Biological Diversity. Oxford, UK: Blackwell Publishing Limited.
20. Team RDC (2011) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria.
21. Dixon P, (2003) Vegan, a package of R functions for community ecology. Journal of Vegetation Science 14: 927-930.
22. Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA, et al. (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 4: e1000255.
23. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
24. Winkel EG, Van Winkelhoff AJ, Timmerman MF, Van der Velden U, Van der Weijden GA, (2001) Amoxicillin plus metronidazole in the treatment of adult periodontitis patients. a double-blind placebo-controlled study. J Clin Periodontol 28: 296-305.
25. Ehmke B, Moter A, Beikler T, Milian E, Flemmig TF, (2005) Adjunctive antimicrobial therapy of periodontitis: long-term effects on disease progression and oral colonization. Periodontol 76: 749-759.
26. Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R, (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 35: e120.
27. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 103: 12115-12120.
28. Sundquist A, Bigdeli S, Jalili R, Druzin ML, Waller S, et al. (2007) Bacterial flora-typing with targeted, chip-based pyrosequencing. BMC Microbiol 7: 108.
29. Huber JA, Morrison HG, Huse SM, Neal PR, Sogin ML, et al. (2009) Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environ Microbiol 11: 1292-1302.
30. Griffen AL, Beall CJ, Campbell JH, Firestone ND, Kumar PS, et al. (2012) Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. ISME J 6(6): 1176-1185.
31. Griffen AL, Beall CJ, Firestone ND, Gross EL, Difranco JM, et al. (2011) CORE: a phylogenetically-curated 16S rDNA database of the core oral microbiome. PLoS One 6: e19051.
32. Kumar PS, Mason MR, Brooker MR, O'Brein K, (2012) Pyrosequencing reveals unique microbial signatures associated with healthy and failing dental implants. J Clin Periodontol 39: 425-433.
33. Socransky SS, Haffajee AD, Cugini MA, Smith C, Kent R Jr, (1998) Microbial complexes in subgingival plaque. J Clin Periodontol 25: 134-144.
34. Socransky SS, Haffajee AD, (2005) Periodontal microbial ecology. Periodontol 2000 38: 135-187.
35. Valenza G, Veihelmann S, Peplies J, Tichy D, Roldan-Pareja MdC, et al. (2009) Microbial changes in periodontitis successfully treated by mechanical plaque removal and systemic amoxicillin and metronidazole. Int J Med Microbiol 299: 427-438.
36. Kolenbrander PE, Palmer RJ, Rickard AH, Jakubocics NS, Chalmers NI, et al. (2006) Bacterial interactions and successions during plaque development. Periodontol 2000 42: 47-79.
37. Beikler T, Prior K, Ehmke B, Flemming T F, (2004) Specific antibiotics in the treatment of periodontitis - a proposed strategy. J Periodontal 75: 169-175.
38. Bernal LA, Guillot E, Paquet C, Mouton C, (1998) Beta-lactamase-producing strains in the species Prevotella intermedia and Prevotella nigrescens. Oral Microbiol Immunol 13: 36-40.
39. Cionca N, Giannopoulou C, Ugolotti G, Mombelli A, (2010) Microbiologic testing and outcomes of full-mouth scaling and root planing with or without amoxicillin/metronidazole in chronic periodontitis. J Periodontal 81: 15-23.
40. Riep B, Edesi-Neuss L, Claessen F, Skarabis H, Ehmke B, et al. (2009) Are putative periodontal pathogens reliable diagnostic markers? J Clin Microbiol 47: 1705-1711.
41. Friedrich MJ, (2008) Microbiome project seeks to understand human body's microscopic residents. JAMA 300: 777-778.
42. Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotech 30: 434-439.