Individuality, stability, and variability of the plaque microbiome

Frontiers in Microbiology

Volumn 7, Issue APR, 2016, Pages

  Utter, Daniel R ^a,b   Mark Welch, Jessica L ^b,c   Borisy, Gary G ^b  

^a HARVARD UNIVERSITY   (United States)

^b FORSYTH INSTITUTE   (United States)

^c MARINE BIOLOGICAL LABORATORY   (United States)

Author keywords

16S rRNA; Community dynamics; Community ecology; Human microbiome; Oral microbiota

Indexed keywords

RNA 16S;

ACTINOMYCES; ARTICLE; CAPNOCYTOPHAGA; CHINESE; COMPARATIVE STUDY; CORYNEBACTERIUM; DATA ANALYSIS; FUSOBACTERIUM; MICROBIOME; NEISSERIA; PREVOTELLA; STREPTOCOCCUS; TOOTH PLAQUE; WESTERN HEMISPHERE;

EID: 84966389839     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2016.00564     Document Type: Article

References (49)

1. Aas, J. A., Paster, B. J., Stokes, L. N., Olsen, I., and Dewhirst, F. E. (2005). Defining the normal bacterial flora of the oral cavity. J. Clin. Microbiol. 43, 5721-5732. doi: 10.1128/JCM.43.11.5721-5732.2005
2. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410. doi: 10.1016/S0022-2836(05)80360-2
3. Ash, C., Farrow, J. A. E., Dorsch, M., Stackebrandt, E., and Collins, M. D. (1991). Comparative analysis of Bacillus anthracis, Bacillus cereus, and related species on the basis of reverse transcriptase sequencing of 16S rRNA. Int. J. Syst. Bacteriol. 41, 343-346. doi: 10.1099/00207713-41-3-343
4. Barrett, S. L. R., Cookson, B. T., Carlson, L. C., Bernard, K. A., and Coyle, M. B. (2001). Diversity within reference strains of Corynebacterium matruchotii includes Corynebacterium durum and a novel organism. J. Clin. Microbiol. 39, 943-948. doi: 10.1128/JCM.39.3.943-948.2001
5. Böddinghaus, B., Wolters, J., Heikens, W., and Böttger, E. C. (1990). Phylogenetic analysis and identification of different serovars of Mycobacterium intracellulare at the molecular level. FEMS Microbiol. Lett. 70, 197-203. doi: 10.1016/S0378-1097(05)80039-4
6. Brandt, B. W., Bonder, M. J., Huse, S. M., and Zaura, E. (2012). TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage. Nucleic Acids Res. 40, W82-W87. doi: 10.1093/nar/gks418
7. Cameron, S. J., Huws, S. A., Hegarty, M. J., Smith, D. P., and Mur, L. A. (2015). The human salivary microbiome exhibits temporal stability in bacterial diversity. FEMS Microbiol. Ecol. 91:fiv091. doi: 10.1093/femsec/fiv091
8. Caporaso, J. G., Bittinger, K., Bushman, F. D., DeSantis, T. Z., Andersen, G. L., and Knight, R. (2010). PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266-267. doi: 10.1093/bioinformatics/btp636
9. Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., et al. (2011). Moving pictures of the human microbiome. Genome Biol. 12:R50. doi: 10.1186/gb-2011-12-5-r50
10. Cilia, V., Lafay, B., and Christen, R. (1996). Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level. Mol. Biol. Evol. 13, 451-461. doi: 10.1093/oxfordjournals.molbev.a025606
11. Clemente, J. C., Pehrsson, E. C., Blaser, M. J., Sandhu, K., Gao, Z., Wang, B., et al. (2015). The microbiome of uncontacted Amerindians. Sci. Adv. 1:e1500183. doi: 10.1126/sciadv.1500183
12. Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., and Knight, R. (2009). Bacterial community variation in human body habitats across space and time. Science 326, 1694-1697. doi: 10.1126/science.1177486
13. David, L. A., Materna, A. C., Friedman, J., Campos-Baptista, M. I., Blackburn, M. C., Perrotta, A., et al. (2014). Host lifestyle affects human microbiota on daily timescales. Genome Biol. 15, 1. doi: 10.1186/gb-2014-15-7-r89
14. Denapaite, D., Brückner, R., Nuhn, M., Reichmann, P., Henrich, B., Maurer, P., et al. (2010). The genome of Streptococcus mitis B6-What is a commensal? PLoS ONE 5:e9426. doi: 10.1371/journal.pone.0009426
15. Dewhirst, F. E., Chen, T., Izard, J., Paster, B. J., Tanner, A. C. R., Yu, W.-H., et al. (2010). The human oral microbiome. J. Bacteriol. 192, 5002-5017. doi: 10.1128/JB.00542-10
16. Diaz, P. I., Zilm, P. S., and Rogers, A. H. (2000). The response to oxidative stress of Fusobacterium nucleatum grown in continuous culture. FEMS Microbiol. Lett. 187, 31-34. doi: 10.1111/j.1574-6968.2000.tb09132.x
17. Ding, T., and Schloss, P. D. (2014). Dynamics and associations of microbial community types across the human body. Nature 509, 357-360. doi: 10.1038/nature13178
18. Eren, A. M., Borisy, G. G., Huse, S. M., and Mark Welch, J. L. (2014). Oligotyping analysis of the human oral microbiome. Proc. Natl. Acad. Sci. U.S.A. 111, E2875-E2884. doi: 10.1073/pnas.1409644111
19. Eren, A. M., Maignien, L., Sul, W. J., Murphy, L. G., Grim, S. L., Morrison, H. G., et al. (2013). Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol. Evol. 4, 1111-1119. doi: 10.1111/2041-210X.12114
20. Eren, A. M., Morrison, H. G., Lescault, P. J., Reveillaud, J., Vineis, J. H., and Sogin, M. L. (2015). Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J. 9, 968-979. doi: 10.1038/ismej.2014.195
21. Faith, J. J., Guruge, J. L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A. L., et al. (2013). The long-term stability of the human gut microbiota. Science 341, 1237439-1237439. doi: 10.1126/science.1237439
22. Flores, G. E., Caporaso, J. G., Henley, J. B., Rideout, J. R., Domogala, D., Chase, J., et al. (2014). Temporal variability is a personalized feature of the human microbiome. Genome Biol. 15, 804. doi: 10.1186/s13059-014-0531-y
23. Fox, G. E., Wisotzkey, J. D., and Jurtshuk, P. Jr. (1992). How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Evol. Microbiol. 42, 166-170. doi: 10.1099/00207713-42-1-166
24. Fukushima, M., Kakinuma, K., and Kawaguchi, R. (2002). Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence. J. Clin. Microbiol. 40, 2779-2785. doi: 10.1128/JCM.40.8.2779-2785.2002
25. Gajer, P., Brotman, R. M., Bai, G., Sakamoto, J., Schütte, U. M. E., Zhong, X., et al. (2012). Temporal dynamics of the human vaginal microbiota. Sci. Transl. Med. 4, 132ra52-132ra52. doi: 10.1126/scitranslmed.3003605
26. Huse, S. M., Dethlefsen, L.es, Huber, J. A., Mark Welch, D., Relman, D. A., and Sogin, M. L. (2008). Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet. 4:e1000255. doi: 10.1371/journal.pgen.1000255
27. Jiang, W.-X., Hu, Y.-J., Gao, L., He, Z.-Y., Zhu, C.-L., Ma, R., et al. (2015). The impact of various time intervals on the supragingival plaque dynamic core microbiome. PLoS ONE 10:e0124631. doi: 10.1371/journal.pone.0124631
28. Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., et al. (2002). Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30, 4432-4441. doi: 10.1093/nar/gkf566
29. Kilian, M., Riley, D. R., Jensen, A., Brüggemann, H., and Tettelin, H. (2014). Parallel evolution of Streptococcus pneumoniae and Streptococcus mitis to pathogenic and mutualistic lifestyles. mBio 5, e01490-14-e01490-14. doi: 10.1128/mbio.01490-14
30. Li, J., Quinque, D., Horz, H.-P., Li, M., Rzhetskaya, M., Raff, J. A., et al. (2014). Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa. BMC Microbiol. 14:316. doi: 10.1186/s12866-014-0316-1
31. Lozupone, C., and Knight, R. (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228-8235. doi: 10.1128/AEM.71.12.8228-8235.2005
32. Mark Welch, J. L., Rossetti, B. J., Rieken, C. W., Dewhirst, F. E., and Borisy, G. G. (2016). Biogeography of a human oral microbiome at the micron scale. Proc. Natl. Acad. Sci. U.S.A. 113, E791-E800. doi: 10.1073/pnas.1522149113
33. Mark Welch, J. L., Utter, D. R., Rossetti, B. J., Mark Welch, D. B., Eren, A. M., and Borisy, G. G. (2014). Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping. Front. Microbiol. 5:568. doi: 10.3389/fmicb.2014.00568
34. Mason, M. R., Nagaraja, H. N., Camerlengo, T., Joshi, V., and Kumar, P. S. (2013). Deep sequencing identifies ethnicity-specific bacterial signatures in the oral microbiome. PLoS ONE 8:e77287. doi: 10.1371/journal.pone.0077287
35. McDonald, D., Price, M. N., Goodrich, J., Nawrocki, E. P., DeSantis, T. Z., Probst, A., et al. (2011). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610-618. doi: 10.1038/ismej.2011.139
36. Nasidze, I., Li, J., Quinque, D., Tang, K., and Stoneking, M. (2009). Global diversity in the human salivary microbiome. Genome Res. 19, 636-643. doi: 10.1101/gr.084616.108
37. Oksanen, J., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O'Hara, R. B., et al. (2013). Vegan: Community Ecology Package. Package version 1.0.1. Available online at: http://cran.r-project.org/web/packages/vegan/index.html. (Accessed July 10, 2015)
38. Park, O. J., Yi, H., Jeon, J. H., Kang, S. S., Koo, K. T., Kum, K. Y., et al. (2015). Pyrosequencing analysis of subgingival microbiota in distinct periodontal conditions. J. Dental Res. 94, 921-927. doi: 10.1177/0022034515583531
39. Perna, N. T., Plunkett, G. III, Burland, V., Mau, B., Glasner, J. D., Rose, D. J., et al. (2001). Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529-533. doi: 10.1038/35054089
40. R Core Team. (2015). R: A Language and Environment for Statistical Computing. Vienna: Foundation for Statistical Computing
41. Ramsey, M. M., Rumbaugh, K. P., and Whiteley, M. (2011). Metabolite cross-feeding enhances virulence in a model polymicrobial infection. PLoS Pathog. 7:e1002012. doi: 10.1371/journal.ppat.1002012
42. Segata, N., Haake, S., Mannon, P., Lemon, K. P., Waldron, L., Gevers, D., et al. (2012). Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol. 13:R42. doi: 10.1186/gb-2012-13-6-r42
43. Stahringer, S. S., Clemente, J. C., Corley, R. P., Hewitt, J., Knights, D., Walters, W. A., et al. (2012). Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood. Genome Res. 22, 2146-2152. doi: 10.1101/gr.140608.112
44. Takeshita, T., Matsuo, K., Furuta, M., Shibata, Y., Fukami, K., Shimazaki, Y., et al. (2014). Distinct composition of the oral indigenous microbiota in South Korean and Japanese adults. Sci. Rep. 4:6990. doi: 10.1038/srep06990
45. The Human Microbiome Project Consortium. (2012). A framework for human microbiome research. Nature 486, 215-221. doi: 10.1038/nature11209
46. Wickham, H. (2009). ggplot2: Elegant Graphics for Data Analysis. New York, NY: Springer
47. Xu, X., He, J., Xue, J., Wang, Y., Li, K., Zhang, K., et al. (2014). Oral cavity contains distinct niches with dynamic microbial communities. Environ. Microbiol. 17, 699-710. doi: 10.1111/1462-2920.12502
48. Zaura, E., Keijser, B. J., Huse, S. M., and Crielaard, W. (2009). Defining the healthy "core microbiome" of oral microbial communities. BMC Microbiol. 9:259. doi: 10.1186/1471-2180-9-259
49. Zhu, L., and Kreth, J. (2012). The role of hydrogen peroxide in environmental adaptation of oral microbial communities. Oxid. Med. Cell. Longev. 2012:717843. doi: 10.1155/2012/717843