Application of metagenomics in understanding oral health and disease

Virulence

Volumn 5, Issue 3, 2014, Pages 424-432

  Xu, Ping ^a   Gunsolley, John ^a  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

Biofilm; Caries; Dental plaque; Metabolic pathway; Metagenomics; Oral microbiome; Pathogen; Periodontal disease; Polymicrobial; Systems biology

Indexed keywords

HOMOSERINE; RNA 16S;

AGGREGATIBACTER; BACILLI; BACTERIAL GENE; BACTERIAL METABOLISM; BIOFILM; CLOSTRIDIA; COMPUTER ANALYSIS; CORYNEBACTERIUM; DNA SEQUENCE; GENETIC DATABASE; HUMAN; LEPTOTRICHIA; LEPTOTRICHIA BUCCALIS; METAGENOMICS; MICROBIOME; MOLECULAR INTERACTION; MOUTH DISEASE; MOUTH FLORA; MOUTH INFECTION; NONHUMAN; ORGANISMAL INTERACTION; PERIODONTITIS; PORPHYROMONAS GINGIVALIS; QUORUM SENSING; REVIEW; RNA SEQUENCE; SEQUENCE ANALYSIS; STREPTOCOCCUS GORDONII; STREPTOCOCCUS MUTANS; STREPTOCOCCUS SANGUINIS; TOOTH PLAQUE; VEILLONELLA PARVULA; HEALTH; HOST PATHOGEN INTERACTION; MICROBIOLOGY; MICROFLORA; SYMBIOSIS;

HOST-PATHOGEN INTERACTIONS; HUMANS; METAGENOMICS; MICROBIOTA; MOUTH DISEASES; ORAL HEALTH; SYMBIOSIS;

EID: 84897932769     PISSN: 21505594     EISSN: 21505608     Source Type: Journal    
DOI: 10.4161/viru.28532     Document Type: Review

References (92)

1. Horz HP, Conrads G. Diagnosis and anti-infective therapy of periodontitis. Expert Rev Anti Infect Ther 2007; 5: 703-15. PMID: 17678 4 31 http://dx.doi.org/10.1586/14787210.5.4.703
2. Selwitz RH, Ismail AI, Pitts NB. Dental caries. Lancet 2007; 369:51-9. PMID:17208642 http://dx.doi.org/10.1016/S0140-6736(07)60031-2
3. Pihlstrom BL, Michalowicz BS, Johnson N W. Periodontal diseases. Lancet 2005; 366:1809-20. PMID:16298220 http://dx.doi.org/10.1016/S0140-6736(05)67728-8
4. Konopka A. What is microbial community ecology? ISME J 2009; 3:1223-30. PMID:19657372 http://dx.doi.org/10.1038/ismej.2009.88
5. 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. PMID:16272510 http://dx.doi.org/10.1128/JCM.43.11.5721-5732.2005
6. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, Lakshmanan A, Wade WG. The human oral microbiome. J Bacteriol 2010; 192:5002-17. PMID:20656903 http://dx.doi.org/10.1128/JB.00542-10
7. Duran-Pinedo AE, Paster B, Teles R, Frias-Lopez J. Correlation network analysis applied to complex biofilm communities. PLoS One 2011; 6:e28438. PMID:22163302 http://dx.doi.org/10.1371/journal.pone.0028438
8. Jenkinson HF. Beyond the oral microbiome. Environ Microbiol 2011; 13:3077-87. PMID:21906224 http://dx.doi.org/10.1111/j.1462-2920.2011.02573.x
9. McLean JS, Fansler SJ, Majors PD, McAteer K, Allen LZ, Shirtliff ME, Lux R, Shi W. Identifying low pH active and lactate-utilizing taxa within oral microbiome communities from healthy children using stable isotope probing techniques. PLoS One 2012; 7:e32219. PMID:22403637 http://dx.doi.org/10.1371/journal.pone.0032219
10. Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, et al. Deep sequencing of the oral microbi-ome reveals signatures of periodontal disease. PLoS One 2012; 7:e37919. PMID:22675498 http://dx.doi.org/10.1371/journal.pone.0037919
11. Ge X, Rodriguez R, Trinh M, Gunsolley J, Xu P. Oral microbiome of deep and shallow dental pockets in chronic periodontitis. PLoS One 2013; 8:e65520. PMID:23762384 http://dx.doi.org/10.1371/journal.pone.0065520
12. Wade WG. The oral microbiome in health and disease. Pharmacol Res 2013; 69:137-43. PMID:23201354 http://dx.doi.org/10.1016/j.phrs.2012.11.006
13. Peterson SN, Snesrud E, Schork NJ, Bretz WA. Dental caries pathogenicity: a genomic and metage-nomic perspective. Int Dent J 2011; 61(Suppl 1):11-22. PMID:21726221 http://dx.doi.org/10.1111/j.1875-595X.2011.00025.x
14. Takahashi N, Nyvad B. The role of bacteria in the caries process: ecological perspectives. J Dent Res 2011; 90:294-303. PMID:20924061 http://dx.doi.org/10.1177/0022034510379602
15. Jenkinson HF, Lamont RJ. Oral microbial communities in sickness and in health. Trends Microbiol 2005; 13:589-95. PMID:16214341 http://dx.doi.org/10.1016/j.tim.2005.09.006
16. Rickard AH, Gilbert P, High NJ, Kolenbrander PE, Handley PS. Bacterial coaggregation: an integral process in the development of multi-species biofilms. Trends Microbiol 2003; 11:94-100. PM I D:1259 813 2 http://dx.doi.org/10.1016/S0966-842X(02)00034-3
17. Nyvad B, Kilian M. Microbiology of the early colonization of human enamel and root surfaces in vivo. Scand J Dent Res 1987; 95:369-80. PMID:3477852
18. Fives-Taylor PM, Meyer DH, Mintz K P, Brissette C. Virulence factors of Actinobacillus actino-mycetemcomitans. Periodontol 2000 1999; 20:136-67. PMID:10522226 http://dx.doi.org/10.1111/j.1600-0757.1999.tb00161.x
19. Témoin S, Wu KL, Wu V, Shoham M, Han YW. Signal peptide of FadA adhesin from Fusobacterium nucleatum plays a novel structural role by modulating the filament's length and width. FEBS Lett 2012; 586:1-6. PMID:22108653 http://dx.doi.org/10.1016/j.febslet.2011.10.047
20. Lamont RJ, Jenkinson HF. Subgingival colonization by Porphyromonas gingivalis. Oral Microbiol Immunol 2000; 15:341-9. PMID:111544 29 http://dx.doi.org/10.1034/j.1399-302x.2000.150601.x
21. Malm S, Jusko M, Eick S, Potempa J, Riesbeck K, Blom AM. Acquisition of complement inhibitor ser-ine protease factor I and its cofactors C4b-binding protein and factor H by Prevotella intermedia. PLoS One 2012; 7:e34852. PMID:22514678 http://dx.doi.org/10.1371/journal.pone.0034852
22. Settem RP, Honma K, Stafford GP, Sharma A. Protein-linked glycans in periodontal bacteria: prevalence and role at the immune interface. Front Microbiol 2013; 4:310. PMID:24146665 http://dx.doi.org/10.3389/fmicb.2013.00310
23. Bian J, Liu X, Cheng YQ, Li C. Inactivation of cyclic Di-GMP binding protein TDE0214 affects the motility, biofilm formation, and virulence of Treponema denticola. J Bacteriol 2013; 195:3897-905. PMID:23794624 http://dx.doi.org/10.1128/JB.00610-13
24. Han Y W, Wang X. Mobile microbiome: oral bacteria in extra-oral infections and inflammation. J Dent Res 2013; 92:485-91. PMID:23625375 http://dx.doi.org/10.1177/0022034513487559
25. Hajishengallis G, Darveau R P, Curtis MA. The keystone-pathogen hypothesis. Nat Rev Microbiol 2 012; 10: 717-25. PMID: 22941505 http://dx.doi.org/10.1038/nrmicro2873
26. Paik S, Senty L, Das S, Noe JC, Munro CL, Kitten T. Identification of virulence determinants for endocarditis in Streptococcus sanguinis by signature-tagged mutagenesis. Infect Immun 2005; 73:6064-74. PMID:16113327 http://dx.doi.org/10.1128/IAI.73.9.6064-6074.2005
27. Xu P, Alves JM, Kitten T, Brown A, Chen Z, Ozaki LS, Manque P, Ge X, Serrano MG, Puiu D, et al. Genome of the opportunistic pathogen Streptococcus sangui-nis. J Bacteriol 2007; 189:3166-75. PMID:17277061 http://dx.doi.org/10.1128/JB.01808-06
28. Paju S, Scannapieco FA. Oral biofilms, periodon-titis, and pulmonary infections. Oral Dis 2007; 13:508-12. PMID:17944664 http://dx.doi.org/10.1111/j.1601-0825.2007.01410a.x
29. Moodley A, Wood NH, Shangase SL. The relationship between periodontitis and diabetes: a brief review. SADJ 2013; 68:260, 262-4. PMID:23971278
30. Han Y W. Oral health and adverse pregnancy outcomes-what's next? J Dent Res 2011; 90:289-93. PMID:21041548 http://dx.doi.org/10.1177/0022034510381905
31. Yeoh N, Burton JP, Suppiah P, Reid G, Stebbings S. The role of the microbiome in rheumatic diseases. Curr Rheumatol Rep 2013; 15:314. PMID:23378145 http://dx.doi.org/10.1007/s11926-012-0314-y
32. Ismail Y, Mahendran V, Octavia S, Day AS, Riordan SM, Grimm MC, Lan R, Lemberg D, Tran TA, Zhang L. Investigation of the enteric pathogenic potential of oral Campylobacter concisus strains isolated from patients with inflammatory bowel disease. PLoS One 2012; 7:e38217. PMID:22666490 http://dx.doi.org/10.1371/journal.pone.0038217
33. Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res 2012; 22:299-306. PMID:22009989 http://dx.doi.org/10.1101/gr.126516.111
34. Palmer RJ Jr. Composition and development of oral bacterial communities. Periodontol 2000 2014; 64:20-39. PMID:24320954 http://dx.doi.org/10.1111/j.160 0-0757.2012.00453.x
35. Schultz-Haudt S, Bruce MA, Bibby BG. Bacterial factors in nonspecific gingivitis. J Dent Res 1954; 33:454-8. PMID:13184032 http://dx.doi.org/10.1177/00220345540330040301
36. MacDonald JB, Sutton RM, Knoll ML, Madlener EM, Grainger RM. The pathogenic components of an experimental fusospirochetal infection. J Infect Dis 1956; 98:15-20. PMID:13295619 http://dx.doi.org/10.1093/infdis/98.1.15
37. Theilade E. The non-specific theory in microbial etiology of inflammatory periodontal diseases. J Clin Periodontol 1986; 13:905-11. PMID:3540019 http://dx.doi.org/10.1111/j.1600-051X.1986.tb01425.x
38. Loesche WJ. Clinical and microbiological aspects of chemotherapeutic agents used according to the specific plaque hypothesis. J Dent Res 1979; 58:2404-12. PMID:41862 http://dx.doi.org/10.1177/00220345790580120905
39. Marsh PD. Microbial ecology of dental plaque and its significance in health and disease. Adv Dent Res 1994; 8:263-71. PMID:7865085
40. Hajishengallis G, Lamont RJ. Beyond the red complex and into more complexity: the polymi-crobial synergy and dysbiosis (PSD) model of periodontal disease etiology. Mol Oral Microbiol 2012; 27:409-19. PMID:23134607 http://dx.doi.org/10.1111/j.2041-1014.2012.00663.x
41. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science 2005; 307:1915-20. PM I D:1579 0 8 4 4 http://dx.doi.org/10.1126/science.1104816
42. Savett DA, Progulske-Fox A. Restriction fragment length polymorphism analysis of two hemaggluti-nin loci, serotyping and agglutinating activity of Porphyromonas gingivalis isolates. Oral Microbiol Immunol 1995; 10:1-7. PMID:7644268 http://dx.doi.org/10.1111/j.1399-302X.1995.tb00110.x
43. Ménard C, Mouton C. Clonal diversity of the taxon Porphyromonas gingivalis assessed by random amplified polymorphic DNA fingerprinting. Infect Immun 1995; 63: 2522-31. PMID:7790065
44. Zijnge V, Harmsen HJ, Kleinfelder J W, van der Rest ME, Degener JE, Welling GW. Denaturing gradient gel electrophoresis analysis to study bacterial community structure in pockets of peri-odontitis patients. Oral Microbiol Immunol 2003; 18:59-65. PMI D:125884 61 http://dx.doi.org/10.1034/j.1399-302X.2003.180110.x
45. Blome B, Braun A, Sobarzo V, Jepsen S. Molecular identification and quantification of bacteria from endodontic infections using real-time polymerase chain reaction. Oral Microbiol Immunol 2008; 23:384-90. PMID:18793361 http://dx.doi.org/10.1111/j.1399-302X.2008.00440.x
46. Colombo A P, Boches SK, Cotton SL, Goodson JM, Kent R, Haffajee AD, Socransky SS, Hasturk H, Van Dyke TE, Dewhirst F, et al. Comparisons of subgin-gival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray. J Periodontol 2009; 80:1421-32. PMID:19722792 http://dx.doi.org/10.1902/jop.2009.090185
47. Sakamoto M, Umeda M, Benno Y. Molecular analysis of human oral microbiota. J Periodontal Res 2005; 40:277-85. PMID: 15 8 539 7 5 http://dx.doi.org/10.1111/j.1600-0765.2005.00793.x
48. Nyvad B, Crielaard W, Mira A, Takahashi N, Beighton D. Dental caries from a molecular microbiological perspective. Caries Res 2013; 47:89-102. PMID:23207320 http://dx.doi.org/10.1159/000345367
49. Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet 2010; 11:31-46. PMID:19997069 http://dx.doi.org/10.1038/nrg2626
50. Zaura E. Next-generation sequencing approaches to understanding the oral microbiome. Adv Dent Res 2012; 24:81-5. PMID:22899686 http://dx.doi.org/10.1177/0022034512449466
51. Burne RA, Zeng L, Ahn SJ, Palmer SR, Liu Y, Lefebure T, Stanhope MJ, Nascimento MM. Progress dissecting the oral microbiome in caries and health. Adv Dent Res 2012; 24:77-80. PMID:22899685 http://dx.doi.org/10.1177/0022034512449462
52. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004; 304:66-74. PMID: 15 0 0171 3 http://dx.doi.org/10.1126/science.1093857
53. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004; 428:37-43. PMID:14961025 http://dx.doi.org/10.1038/nature02340
54. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, et al. Comparative metagenomics of microbial communities. Science 2005; 308:554-7. PMID:15845853 http://dx.doi.org/10.1126/science.1107851
55. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human micro-biome. Nature 2012; 486:207-14. PMID:22699609 http://dx.doi.org/10.1038/nature11234
56. Human Microbiome Project Consortium. A framework for human microbiome research. Nature 2012; 486:215-21. PMID: 22699610 http://dx.doi.org/10.1038/nature11209
57. Dark MJ. Whole-genome sequencing in bacteriology: state of the art. Infect Drug Resist 2013; 6:115-23. PMID: 24143115 http://dx.doi.org/10.2147/IDR.S35710
58. Dewhirst FE, Klein EA, Thompson EC, Blanton JM, Chen T, Milella L, Buckley CM, Davis IJ, Bennett ML, Marshall-Jones ZV. The canine oral microbi-ome. PLoS One 2012; 7:e36067. PMID:22558330 http://dx.doi.org/10.1371/journal.pone.0036067
59. Griffen AL, Beall CJ, Campbell JH, Firestone ND, Kumar PS, Yang ZK, Podar M, Leys EJ. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. ISME J 2012; 6: 1176-85. PMID:22170420 http://dx.doi.org/10.1038/ismej.2011.191
60. Jiang W, Zhang J, Chen H. Pyrosequencing analysis of oral microbiota in children with severe early childhood dental caries. Curr Microbiol 2013; 67:537-42. PMID:23743597 http://dx.doi.org/10.1007/s00284-013-0393-7
61. Simón-Soro A, Tomás I, Cabrera-Rubio R, Catalan MD, Ny vad B, Mira A. Microbia l geography of the oral cavity. J Dent Res 2013; 92:616-21. P MID: 2 3 6 74 2 6 3 http://dx.doi.org/10.1177/0022034513488119
62. Jiang B, Liang X, Chen Y, Ma T, Liu L, Li J, Jiang R, Chen T, Zhang X, Li S. Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome. Sci Rep 2012; 2:936. PMID:23226834
63. Kraneveld EA, Buijs MJ, Bonder MJ, Visser M, Keijser BJ, Crielaard W, Zaura E. The relation between oral Candida load and bacterial micro-biome profiles in Dutch older adults. PLoS One 2012; 7:e42770. PMID:22900048 http://dx.doi.org/10.1371/journal.pone.0042770
64. Hsiao W W, Li KL, Liu Z, Jones C, Fraser-Liggett CM, Fouad AF. Microbial transformation from normal oral microbiota to acute endodontic infections. BMC Genomics 2012; 13:345. PMID:22839737 http://dx.doi.org/10.1186/1471-2164-13-345
65. Pinto AJ, Raskin L. PCR biases distort bacterial and archaeal community structure in pyro-sequencing datasets. PLoS One 2012; 7:e43093. PMID:22905208 http://dx.doi.org/10.1371/journal.pone.0043093
66. Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007; 10:504-9. PMID:17923431 http://dx.doi.org/10.1016/j.mib.2007.08.006
67. Faruque SM, Mekalanos JJ. Pathogenicity islands and phages in Vibrio cholerae evolution. Trends Microbiol 20 03; 11:505-10. PMID:14607067 http://dx.doi.org/10.1016/j.tim.2003.09.003
68. Lesic B, Carniel E. Horizontal transfer of the high-pathogenicity island of Yersinia pseudotuberculosis. J Bacteriol 2005; 187:3352-8. P M I D: 15 8 6 6 9 1 9 http://dx.doi.org/10.1128/JB.187.10.3352-3358.2005
69. Malachowa N, DeLeo FR. Mobile genetic elements of Staphylococcus aureus. Cell Mol Life Sci 2010; 67:3057-71. PMID:20668911 http://dx.doi.org/10.1007/s00018-010-0389-4
70. Thomas T, Gilbert J, Meyer F. Metagenomics-a guide from sampling to data analysis. Microb Inform Exp 2012; 2:3. PMID:22587947 http://dx.doi.org/10.1186/2042-5783-2-3
71. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. [see comments]. Science 1995; 269: 496-512. PMID:7542800 http://dx.doi.org/10.1126/science.7542800
72. 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. PMI D:20624719 http://dx.doi.org/10.1093/database/baq013
73. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A 2005; 102:13950-5. PMID:16172379 http://dx.doi.org/10.1073/pnas.0506758102
74. Cornejo OE, Lefébure T, Bitar PD, Lang P, Richards V P, Eilertson K, Do T, Beighton D, Zeng L, Ahn SJ, et al. Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Mol Biol Evol 2013; 30:881-93. PMID:23228887 http://dx.doi.org/10.1093/molbev/mss278
75. Xie G, Chain PS, Lo CC, Liu KL, Gans J, Merritt J, Qi F. Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing. Mol Oral Microbiol 2010; 25:391-405. PMID:21040513 http://dx.doi.org/10.1111/j.20 41-1014.2010.00587.x
76. Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep 2013; 3:1843. PMID:23673380
77. Yoshino T, Laine ML, van Winkelhoff AJ, Dahlén G. Genotype variation and capsular serotypes of Porphyromonas gingivalis from chronic periodontitis and periodontal abscesses. FEMS Microbiol Lett 2007; 270:75-81. PMID:17439635 http://dx.doi.org/10.1111/j.1574-6968.2007.0 0651.x
78. Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, Simón-Soro A, Pignatelli M, Mira A. The oral metagenome in health and disease. ISME J 2012; 6:46-56. PMID:21716308 http://dx.doi.org/10.1038/ismej.2011.85
79. Noorda WD, Purdell-Lewis DJ, van Montfort AM, Weerkamp AH. Monobacterial and mixed bacterial plaques of Streptococcus mutans and Veillonella alcalescens in an artificial mouth: development, metabolism, and effect on human dental enamel. Caries Res 1988; 22:342-7. PMID:3214847 http://dx.doi.org/10.1159/000261134
80. Gross EL, Leys EJ, Gasparovich SR, Firestone ND, Schwartzbaum JA, Janies DA, Asnani K, Griffen AL. Bacterial 16S sequence analysis of severe caries in young permanent teeth. J Clin Microbiol 2010; 48:4121-8. PMID:20826648 http://dx.doi.org/10.1128/JCM.01232-10
81. Merritt J, Qi F. The mutacins of Streptococcus mutans: regulation and ecology. Mol Oral Microbiol 2012; 27:57-69. PMID:22394465 http://dx.doi.org/10.1111/j.2041-1014.2011.00634.x
82. Campan P, Planchand PO, Duran D. Pilot study on n-3 polyunsaturated fatty acids in the treatment of human experimental gingivitis. J Clin Periodontol 1997; 24:907-13. PMID:9442428 http://dx.doi.org/10.1111/j.1600-051X.1997.tb01210.x
83. Kesavalu L, Bakthavatchalu V, Rahman MM, Su J, Raghu B, Dawson D, Fernandes G, Ebersole JL. Omega-3 fatty acid regulates inflammatory cytokine/mediator messenger RNA expression in Porphyromonas gingivalis-induced experimental periodontal disease. Oral Microbiol Immunol 2007; 22:232-9. PMID:17600534 http://dx.doi.org/10.1111/j.1399-302X.2007.00346.x
84. Jain S, Darveau R P. Contribution of Porphyromonas gingivalis lipopolysaccharide to periodontitis. Periodontol 2000 2010; 54:53-70. PMID:20712633 http://dx.doi.org/10.1111/j.1600-0757.2009.00333.x
85. Caufield PW, Dasanayake A P, Li Y, Pan Y, Hsu J, Hardin JM. Natural history of Streptococcus sangui-nis in the oral cavity of infants: evidence for a discrete window of infectivity. Infect Immun 2000; 68:4018-23. PMID:10858217 http://dx.doi.org/10.1128/IAI.68.7.4018-4023.2000
86. Kreth J, Merritt J, Shi W, Qi F. Competition and coexistence between Streptococcus mutans and Streptococcus sanguinis in the dental biofilm. J Bacteriol 2005; 187:7193-203. PMID:16237003 http://dx.doi.org/10.1128/JB.187.21.7193-7203.2005
87. Chen L, Ge X, Dou Y, Wang X, Patel JR, Xu P. Identification of hydrogen peroxide production-related genes in Streptococcus sanguinis and their functional relationship with pyruvate oxidase. Microbiology 2011; 157:13-20. PMID:20847003 http://dx.doi.org/10.1099/mic.0.039669-0
88. Jagtap P, McGowan T, Bandhakavi S, Tu ZJ, Seymour S, Griffin TJ, Rudney JD. Deep meta-proteomic analysis of human salivary supernatant. Proteomics 2012; 12:992-1001. PMID:22522805 http://dx.doi.org/10.1002/pmic.201100503
89. Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P. Prediction of effective genome size in metagenomic samples. Genome Biol 2007; 8:R10. PMID:17224063 http://dx.doi.org/10.1186/gb-2007-8-1-r10
90. Hunter SJ, Easton S, Booth V, Henderson B, Wade WG, Ward JM. Selective removal of human DNA from metagenomic DNA samples extracted from dental plaque. J Basic Microbiol 2011; 51:442-6. PMID:21298692 http://dx.doi.org/10.1002/jobm.201000372
91. Mullany P, Hunter S, Allan E. Metagenomics of dental biofilms. Adv Appl Microbiol 2008; 64:125-36. PMID:18485283 http://dx.doi.org/10.1016/S0065-2164(08)00404-8
92. Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C. Computational meta'omics for microbial community studies. Mol Syst Biol 2013; 9:666. PMID:23670539 http://dx.doi.org/10.1038/msb.2013.22