Transcriptome analysis of bacteriophage communities in periodontal health and disease

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Santiago Rodriguez, Tasha M ^a   Naidu, Mayuri ^a   Abeles, Shira R ^b   Boehm, Tobias K ^c   Ly, Melissa ^a   Pride, David T ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c WESTERN UNIVERSITY OF HEALTH SCIENCES   (United States)

Author keywords

Bacteriophage; Metagenome; Microbiome; Periodontal Disease; Periodontitis; Saliva; Transcriptome; Virome

Indexed keywords

INTEGRASE; TRANSCRIPTOME; VIRAL PROTEIN;

ARTICLE; BACTERIOPHAGE; CLINICAL ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; HEALTH STATUS; HUMAN; MICROBIOME; MOUTH CAVITY; NONHUMAN; ORGANISM COMMUNITY; PERIODONTAL DISEASE; PROPHAGE; PROTEIN EXPRESSION; RNA SEQUENCE; VIRUS COMMUNITY; VIRUS GENE; VIRUS IDENTIFICATION; VIRUS TRANSCRIPTION; CLASSIFICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; LYSOGENIZATION; MOUTH; PHYSIOLOGY; PROCEDURES; SEQUENCE ANALYSIS; VIROLOGY;

BACTERIA (MICROORGANISMS); FIRMICUTES;

BACTERIOPHAGES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, VIRAL; HUMANS; LYSOGENY; MOUTH; PERIODONTAL DISEASES; SEQUENCE ANALYSIS, RNA; VIRAL PROTEINS;

EID: 85019237162     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1781-0     Document Type: Article

References (55)

1. Eke PI, Thornton-Evans G, Dye B, Genco R. Advances in surveillance of periodontitis: the Centers for Disease Control and Prevention periodontal disease surveillance project. J Periodontol. 2012;83:1337-42.
2. Gocke C, Holtfreter B, Meisel P, Grotevendt A, Jablonowski L, Nauck M, et al. Abdominal obesity modifies long-term associations between periodontitis and markers of systemic inflammation. Atherosclerosis. 2014;235:351-7.
3. Bokhari SA, Khan AA, Butt AK, Hanif M, Izhar M, Tatakis DN, et al. Periodontitis in coronary heart disease patients: strong association between bleeding on probing and systemic biomarkers. J Clin Periodontol. 2014;41(11):1048-54.
4. Suvan J, D'Aiuto F, Moles DR, Petrie A, Donos N. Association between overweight/obesity and periodontitis in adults. A systematic review. Obes Rev. 2011;12:e381-404.
5. Patel MD, Shakir QJ, Shetty A. Interrelationship between chronic periodontitis and anemia: a 6-month follow-up study. J Indian Soc Periodontol. 2014;18:19-25.
6. Perayil J, Suresh N, Fenol A, Vyloppillil R, Bhaskar A, Menon S. Comparison of Hba1c levels in non-diabetic healthy subjects and subjects with periodontitis before and after non-surgical periodontal therapy. J Periodontol. 2014;1-17.
7. Raman RP, Taiyeb-Ali TB, Chan SP, Chinna K, Vaithilingam RD. Effect of nonsurgical periodontal therapy verses oral hygiene instructions on Type 2 diabetes subjects with chronic periodontitis: a randomised clinical trial. BMC Oral Health. 2014;14:79.
8. Corbella S, Francetti L, Taschieri S, De Siena F, Fabbro MD. Effect of periodontal treatment on glycemic control of patients with diabetes: a systematic review and meta-analysis. J Diabetes Investig. 2013;4:502-9.
9. Darveau RP, Hajishengallis G, Curtis MA. Porphyromonas gingivalis as a potential community activist for disease. J Dent Res. 2012;91:816-20.
10. Gersdorf H, Meissner A, Pelz K, Krekeler G, Gobel UB. Identification of Bacteroides forsythus in subgingival plaque from patients with advanced periodontitis. J Clin Microbiol. 1993;31:941-6.
11. Ximenez-Fyvie LA, Haffajee AD, Socransky SS. Microbial composition of supra- and subgingival plaque in subjects with adult periodontitis. J Clin Periodontol. 2000;27:722-32.
12. Fine DH, Markowitz K, Fairlie K, Tischio-Bereski D, Ferrendiz J, Furgang D, et al. A consortium of Aggregatibacter actinomycetemcomitans, Streptococcus parasanguinis, and Filifactor alocis is present in sites prior to bone loss in a longitudinal study of localized aggressive periodontitis. J Clin Microbiol. 2013;51:2850-61.
13. Loesche WJ. Role of Streptococcus mutans in human dental decay. Microbiol Rev. 1986;50:353-80.
14. Sela MN. Role of Treponema denticola in periodontal diseases. Crit Rev Oral Biol Med. 2001;12:399-413.
15. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007;449:804-10.
16. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312:1355-9.
17. Huse SM, Ye Y, Zhou Y, Fodor AA. A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS One. 2012;7, e34242.
18. Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol. 2005;43:5721-32.
19. Eckburg PB, Lepp PW, Relman DA. Archaea and their potential role in human disease. Infect Immun. 2003;71:591-6.
20. Ding T, Schloss PD. Dynamics and associations of microbial community types across the human body. Nature. 2014;509:357-60.
21. Pride DT, Salzman J, Haynes M, Rohwer F, Davis-Long C, White 3rd RA, et al. Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J. 2012;6:915-26.
22. Willner D, Furlan M, Schmieder R, Grasis JA, Pride DT, Relman DA, et al. Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Proc Natl Acad Sci U S A. 2011;108 Suppl 1:4547-53.
23. Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, Salamon P, et al. Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol. 2003;185:6220-3.
24. Breitbart M, Haynes M, Kelley S, Angly F, Edwards RA, Felts B, et al. Viral diversity and dynamics in an infant gut. Res Microbiol. 2008;159:367-73.
25. Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, Simon-Soro A, Pignatelli M, et al. The oral metagenome in health and disease. ISME J. 2012;6:46-56.
26. Lepp PW, Brinig MM, Ouverney CC, Palm K, Armitage GC, Relman DA. Methanogenic Archaea and human periodontal disease. Proc Natl Acad Sci U S A. 2004;101:6176-81.
27. Griffen AL, Beall CJ, Campbell JH, Firestone ND, Kumar PS, Yang ZK, et al. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. ISME J. 2012;6:1176-85.
28. Abusleme L, Dupuy AK, Dutzan N, Silva N, Burleson JA, Strausbaugh LD, et al. The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. ISME J. 2013;7:1016-25.
29. Li Y, He J, He Z, Zhou Y, Yuan M, Xu X, et al. Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients. ISME J. 2014;8(9):1879-91.
30. Belstrom D, Fiehn NE, Nielsen CH, Kirkby N, Twetman S, Klepac-Ceraj V, et al. Differences in bacterial saliva profile between periodontitis patients and a control cohort. J Clin Periodontol. 2014;41:104-12.
31. Ly M, Abeles SR, Boehm TK, Robles-Sikisaka R, Naidu M, Santiago-Rodriguez T, et al. Altered oral viral ecology in association with periodontal disease. MBio. 2014;5:e01133-01114.
32. Cappuyns I, Gugerli P, Mombelli A. Viruses in periodontal disease - a review. Oral Dis. 2005;11:219-29.
33. Imbronito AV, Okuda OS, Maria de Freitas N, Moreira Lotufo RF, Nunes FD. Detection of herpesviruses and periodontal pathogens in subgingival plaque of patients with chronic periodontitis, generalized aggressive periodontitis, or gingivitis. J Periodontol. 2008;79:2313-21.
34. Chalabi M, Rezaie F, Moghim S, Mogharehabed A, Rezaei M, Mehraban B. Periodontopathic bacteria and herpesviruses in chronic periodontitis. Mol Oral Microbiol. 2010;25:236-40.
35. Stein JM, Said Yekta S, Kleines M, Ok D, Kasaj A, Reichert S, et al. Failure to detect an association between aggressive periodontitis and the prevalence of herpesviruses. J Clin Periodontol. 2013;40:1-7.
36. Naidu M, Robles-Sikisaka R, Abeles SR, Boehm TK, Pride DT. Characterization of bacteriophage communities and CRISPR profiles from dental plaque. BMC Microbiol. 2014;14:175.
37. Abeles SR, Robles-Sikisaka R, Ly M, Lum AG, Salzman J, Boehm TK, et al. Human oral viruses are personal, persistent and gender-consistent. ISME J. 2014;8(9):1753-67.
38. Jorth P, Turner KH, Gumus P, Nizam N, Buduneli N, Whiteley M. Metatranscriptomics of the human oral microbiome during health and disease. MBio. 2014;5:e01012-01014.
39. Kebschull M, Demmer RT, Grun B, Guarnieri P, Pavlidis P, Papapanou PN. Gingival tissue transcriptomes identify distinct periodontitis phenotypes. J Dent Res. 2014;93:459-68.
40. Lucchini S, Desiere F, Brussow H. Similarly organized lysogeny modules in temperate Siphoviridae from low GC content gram-positive bacteria. Virology. 1999;263:427-35.
41. Sandaa RA. Environmental Viral Pool. In: Schmidt TM, Schaechter M, editors. Topics in Environmental and Ecological Microbiology. Elsevier; 2012. p.101-3.
42. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, et al. The marine viromes of four oceanic regions. PLoS Biol. 2006;4, e368.
43. Choi J, Kotay SM, Goel R. Various physico-chemical stress factors cause prophage induction in Nitrosospira multiformis 25196-an ammonia oxidizing bacteria. Water Res. 2010;44:4550-8.
44. Chavez de Paz LE, Bergenholtz G, Dahlen G, Svensater G. Response to alkaline stress by root canal bacteria in biofilms. Int Endod J. 2007;40:344-55.
45. Robles-Sikisaka R, Ly M, Boehm T, Naidu M, Salzman J, Pride DT. Association between living environment and human oral viral ecology. ISME J. 2013;7:1710-24.
46. Robles-Sikisaka R, Naidu M, Ly M, Salzman J, Abeles SR, Boehm TK, et al. Conservation of streptococcal CRISPRs on human skin and saliva. BMC Microbiol. 2014;14:146.
47. Wang IN, Smith DL, Young R. Holins: the protein clocks of bacteriophage infections. Annu Rev Microbiol. 2000;54:799-825.
48. Catalão MJ, Gil F, Moniz-Pereira J, Sao-Jose C, Pimentel M. Diversity in bacterial lysis systems: bacteriophages show the way. FEMS Microbiol Rev. 2013;37:554-71.
49. Barr JJ, Auro R, Furlan M, Whiteson KL, Erb ML, Pogliano J, et al. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A. 2013;110:10771-6.
50. Loe H. The gingival index, the plaque index and the retention index systems. J Periodontol. 1967;38:Suppl:610-6.
51. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011;475:348-52.
52. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:386.
53. Rohwer F, Edwards R. The Phage Proteomic Tree: a genome-based taxonomy for phage. J Bacteriol. 2002;184:4529-35.
54. Saldanha AJ. Java Treeview--extensible visualization of microarray data. Bioinformatics. 2004;20:3246-8.
55. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335-6.