Characterization of bacteriophage communities and CRISPR profiles from dental plaque

BMC Microbiology

David T Pride¹  Tobias K Boehm³  Shira R Abeles¹  Refugio Robles-Sikisaka²  Mayuri Naidu² 

[1]Department of Medicine, University of California, San Diego, CA, USA

[2]Department of Pathology, University of California, San Diego, CA, USA

[3]College of Dental Medicine, Western University of Health Sciences, Pomona, CA, USA

关键词: CRISPR;    Dental plaque;    Microbiome;    Virome;    Virus;    Oral biofilm;   

Others  :  1140854
DOI  :  10.1186/1471-2180-14-175

 received in 2013-09-24, accepted in 2014-06-26,  发布年份 2014

【 摘 要 】

Background

Dental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether plaque was populated by viral communities, and whether there were differences in viral communities specific to subject or sample type.

Results

We found that the plaque was inhabited by a community of bacteriophage whose membership was mostly subject-specific. There was a significant proportion of viral homologues shared between plaque and salivary viromes within each subject, suggesting that some oral viruses were present in both sites. We also characterized Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in oral streptococci, as their profiles provide clues to the viruses that oral bacteria may be able to counteract. While there were some CRISPR spacers specific to each sample type, many more were shared across sites and were highly subject specific. Many CRISPR spacers matched viruses present in plaque, suggesting that the evolution of CRISPR loci may have been specific to plaque-derived viruses.

Conclusions

Our findings of subject specificity to both plaque-derived viruses and CRISPR profiles suggest that human viral ecology may be highly personalized.

【 授权许可】

   
2014 Naidu et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Figure 7.

【 参考文献 】

• [1]Bik EM, Long CD, Armitage GC, Loomer P, Emerson J, Mongodin EF, Nelson KE, Gill SR, Fraser-Liggett CM, Relman DA: Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J 2010, 4(8):962-974.
• [2]Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R: Bacterial community variation in human body habitats across space and time. Science 2009, 326(5960):1694-1697.
• [3]Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA: Diversity of the human intestinal microbial flora. Science 2005, 308(5728):1635-1638.
• [4]Gao Z, Tseng CH, Pei Z, Blaser MJ: Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A 2007, 104(8):2927-2932.
• [5]Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD: The human gut virome: inter-individual variation and dynamic response to diet. Genome Res 2011, 21(10):1616-1625.
• [6]Pride DT, Salzman J, Relman DA: Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses. Environ Microbiol 2012, 14(9):2564-2576.
• [7]Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI: Viruses in the faecal microbiota of monozytotic twins and their mothers. Nature 2010, 466(7304):334-338.
• [8]Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F: Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One 2009, 4(10):e7370.
• [9]Willner D, Furlan M, Schmieder R, Grasis JA, Pride DT, Relman DA, Angly FE, McDole T, Mariella RP Jr, Rohwer F, Haynes M: Microbes and health sackler colloquium: metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Proc Natl Acad Sci U S A 2011, 108(Suppl 1):4547-4553.
• [10]Pride DT, Salzman J, Haynes M, Rohwer F, Davis-Long C, White RA 3rd, Loomer P, Armitage GC, Relman DA: Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J 2012, 6(5):915-926.
• [11]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(9):1710-1724.
• [12]Foulongne V, Sauvage V, Hebert C, Dereure O, Cheval J, Gouilh MA, Pariente K, Segondy M, Burguiere A, Manuguerra JC, Caro V, Eloit M: Human skin microbiota: high diversity of DNA viruses identified on the human skin by high throughput sequencing. PLoS One 2012, 7(6):e38499.
• [13]Minot S, Grunberg S, Wu GD, Lewis JD, Bushman FD: Hypervariable loci in the human gut virome. Proc Natl Acad Sci U S A 2012, 109(10):3962-3966.
• [14]Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, Salamon P, Rohwer F: Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 2003, 185(20):6220-6223.
• [15]Carlsson J: Bacterial metabolism in dental biofilms. Adv Dent Res 1997, 11(1):75-80.
• [16]Belay N, Johnson R, Rajagopal BS, de Macario EC, Daniels L: Methanogenic bacteria from human dental plaque. Appl Environ Microbiol 1988, 54(2):600-603.
• [17]Zhou Y, Gao H, Mihindukulasuriya KA, Rosa PS, Wylie KM, Vishnivetskaya T, Podar M, Warner B, Tarr PI, Nelson DE, Fortenberry JD, Holland MJ, Burr SE, Shannon WD, Sodergren E, Weinstock GM: Biogeography of the ecosystems of the healthy human body. Genome Biol 2013, 14(1):R1. BioMed Central Full Text
• [18]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(16):6176-6181.
• [19]Al-Jarbou AN: Genomic library screening for viruses from the human dental plaque revealed pathogen-specific lytic phage sequences. Curr Microbiol 2012, 64(1):1-6.
• [20]Hitch G, Pratten J, Taylor PW: Isolation of bacteriophages from the oral cavity. Lett Appl Microbiol 2004, 39(2):215-219.
• [21]Willi K, Sandmeier H, Asikainen S, Saarela M, Meyer J: Occurrence of temperate bacteriophages in different Actinobacillus actinomycetemcomitans serotypes isolated from periodontally healthy individuals. Oral Microbiol Immunol 1997, 12(1):40-46.
• [22]Adler CJ, Dobney K, Weyrich LS, Kaidonis J, Walker AW, Haak W, Bradshaw CJ, Townsend G, Soltysiak A, Alt KW, Parkhill J, Cooper A: Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat Genet 2013, 45(4):450-455.
• [23]Duran-Pinedo AE, Paster B, Teles R, Frias-Lopez J: Correlation network analysis applied to complex biofilm communities. PLoS One 2011, 6(12):e28438.
• [24]Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S: Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One 2012, 7(6):e37919.
• [25]Alcaraz LD, Belda-Ferre P, Cabrera-Rubio R, Romero H, Simon-Soro A, Pignatelli M, Mira A: Identifying a healthy oral microbiome through metagenomics. Clin Microbiol Infect 2012, 18(Suppl 4):54-57.
• [26]Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, Simon-Soro A, Pignatelli M, Mira A: The oral metagenome in health and disease. ISME J 2012, 6(1):46-56.
• [27]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.
• [28]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.
• [29]Peterson SN, Snesrud E, Liu J, Ong AC, Kilian M, Schork NJ, Bretz W: The dental plaque microbiome in health and disease. PLoS One 2013, 8(3):e58487.
• [30]Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H, Mahaffy JM, Mueller JE, Nulton J, Olson R, Parsons R, Rayhawk S, Suttle CA, Rohwer F: The marine viromes of four oceanic regions. PLoS Biol 2006, 4(11):e368.
• [31]Bench SR, Hanson TE, Williamson KE, Ghosh D, Radosovich M, Wang K, Wommack KE: Metagenomic characterization of Chesapeake Bay virioplankton. Appl Environ Microbiol 2007, 73(23):7629-7641.
• [32]Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P: CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007, 315(5819):1709-1712.
• [33]Garneau JE, Dupuis ME, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadan AH, Moineau S: The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 2010, 468(7320):67-71.
• [34]Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J: Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 2008, 321(5891):960-964.
• [35]Pride DT, Sun CL, Salzman J, Rao N, Loomer P, Armitage GC, Banfield JF, Relman DA: Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Res 2011, 21(1):126-136.
• [36]Haynes M, Rohwer F: The Human Virome. In Metagenomics of the Human Body. Edited by Nelson KE. New York, NY: Springer; 2011:351.
• [37]Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, et al.: An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475(7356):348-352.
• [38]Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV: Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 2011, 9(6):467-477.
• [39]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.
• [40]Ximenez-Fyvie LA, Haffajee AD, Socransky SS: Comparison of the microbiota of supra- and subgingival plaque in health and periodontitis. J Clin Periodontol 2000, 27(9):648-657.
• [41]Paster BJ, Boches SK, Galvin JL, Ericson RE, Lau CN, Levanos VA, Sahasrabudhe A, Dewhirst FE: Bacterial diversity in human subgingival plaque. J Bacteriol 2001, 183(12):3770-3783.
• [42]Barr JJ, Auro R, Furlan M, Whiteson KL, Erb ML, Pogliano J, Stotland A, Wolkowicz R, Cutting AS, Doran KS, Salamon P, Youle M, Rohwer F: Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A 2013, 110(26):10771-10776.
• [43]Loe H: The gingival index, the plaque index and the retention index systems. J Periodontol 1967, 38(6):610-616.
• [44]Noble RT, Fuhrman JA: Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat Microb Ecol 1998, 14:113-118.
• [45]Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM: The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009, 37(Database issue):D141-D145.
• [46]DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL: Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006, 72(7):5069-5072.
• [47]Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013, 41(Database issue):D590-D596.
• [48]Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F: Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A 2002, 99(22):14250-14255.
• [49]Saldanha AJ: Java Treeview–extensible visualization of microarray data. Bioinformatics 2004, 20(17):3246-3248.
• [50]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.
• [51]Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504.
• [52]Stothard P, Wishart DS: Circular genome visualization and exploration using CGView. Bioinformatics 2005, 21(4):537-539.