The effects of family, dentition, and dental caries on the salivary microbiome

Annals of Epidemiology

Volumn 26, Issue 5, 2016, Pages 348-354

  Foxman, Betsy ^a   Luo, Ting ^a   Srinivasan, Usha ^a   Ramadugu, Kirtana ^a   Wen, Ai ^b   Goldberg, Deborah ^a   Shedden, Kerby ^a   Crout, Richard ^c,d   McNeil, Daniel W ^c,d   Weyant, Robert ^d   Marazita, Mary L ^d  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF NORTHERN IOWA   (United States)

^c WEST VIRGINIA UNIVERSITY   (United States)

^d UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

Dental caries; Family; Salivary microbiome

Indexed keywords

DNA; RNA 16S;

ADOLESCENT; ADULT; ARTICLE; CHILD; COHORT ANALYSIS; DENTAL CARIES; DENTITION; DNA EXTRACTION; ESCHERICHIA COLI; FAMILY; FAMILY HEALTH; FEMALE; GENE SEQUENCE; HUMAN; LACTOBACILLUS; MAJOR CLINICAL STUDY; MALE; MOUTH FLORA; NONHUMAN; PEPTONIPHILUS; PRESCHOOL CHILD; PRIORITY JOURNAL; PROPIONIBACTERIUM; SALIVA ANALYSIS; TAXONOMY; AGING; COMPARATIVE STUDY; GENETIC PREDISPOSITION; GENETICS; HEALTH; MICROBIOLOGY; MICROFLORA; MIDDLE AGED; PHYSIOLOGY; RISK FACTOR; SALIVA; SALIVARY GLAND; SPECIMEN HANDLING; UNITED STATES;

ADOLESCENT; ADULT; AGING; APPALACHIAN REGION; CHILD; CHILD, PRESCHOOL; COHORT STUDIES; DENTAL CARIES; DENTITION; FAMILY; FEMALE; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MALE; MICROBIOTA; MIDDLE AGED; ORAL HEALTH; RISK FACTORS; RNA, RIBOSOMAL, 16S; SALIVA; SALIVARY GLANDS; SAMPLING STUDIES; SPECIMEN HANDLING;

EID: 84964883819     PISSN: 10472797     EISSN: 18732585     Source Type: Journal    
DOI: 10.1016/j.annepidem.2016.03.006     Document Type: Article

References (32)

1. [1] Yoshizawa, J.M., Schafer, C.A., Schafer, J.J., Farrell, J.J., Paster, B.J., Wong, D.T., Salivary biomarkers: toward future clinical and diagnostic utilities. Clin Microbiol Rev 26:4 (2013), 781–791.
2. [2] Lazarevic, V., Whiteson, K., Hernandez, D., François, P., Schrenzel, J., Study of inter- and intra-individual variations in the salivary microbiota. BMC Genomics, 11, 2010, 523.
3. [3] Zhou, Y., Gao, H., Mihindukulasuriya, K.A., Wylie, K.M., Vishnivetskaya, T., Podar, M., et al. Biogeography of the ecosystems of the healthy human body. Genome Biol, 14(1), 2013, R1.
4. [4] Nasidze, I., Li, J., Quinque, D., Tang, K., Stoneking, M., Global diversity in the human salivary microbiome. Genome Res 19:4 (2009), 636–643.
5. [5] De Filippis, F., Vannini, L., La Storia, A., Laghi, L., Piombino, P., Stellato, G., et al. The same microbiota and a potentially discriminant metabolome in the saliva of omnivore, ovo-lacto-vegetarian and vegan individuals. PLoS One, 9(11), 2014, e112373.
6. [6] Belstrøm, D., Fiehn, N.E., Nielsen, C.H., Holmstrup, P., Kirkby, N., Klepac-Ceraj, V., et al. Altered bacterial profiles in saliva from adults with caries lesions: a case-cohort study. Caries Res 48:5 (2014), 368–375.
7. [7] Yang, F., Zeng, X., Ning, K., Liu, K.L., Lo, C.C., Wang, W., et al. Saliva microbiomes distinguish caries-active from healthy human populations. ISME J 6:1 (2012), 1–10.
8. [8] Luo, A.H., Yang, D.Q., Xin, B.C., Paster, B.J., Qin, J., Microbial profiles in saliva from children with and without caries in mixed dentition. Oral Dis 18:6 (2012), 595–601.
9. [9] Nalliah, R.P., Allareddy, V., Elangovan, S., Karimbux, N., Allareddy, V., Hospital based emergency department visits attributed to dental caries in the United States in 2006. J Evid Based Dent Pract 10:4 (2010), 212–222.
10. [10] Sheiham, A., James, W.P., Diet and dental caries: the pivotal role of free sugars reemphasized. J Dent Res 94:10 (2015), 1341–1347.
11. [11] Shaffer, J.R., Wang, X., McNeil, D.W., Weyant, R.J., Crout, R., Marazita, M.L., Genetic susceptibility to dental caries differs between the sexes: a family-based study. Caries Res 49:2 (2015), 133–140.
12. [12] Belstrøm, D., Holmstrup, P., Nielsen, C.H., Kirkby, N., Twetman, S., Heitmann, B.L., et al. Bacterial profiles of saliva in relation to diet, lifestyle factors, and socioeconomic status. J Oral Microbiol, 6, 2014.
13. [13] Song, S.J., Lauber, C., Costello, E.K., Lozupone, C.A., Humphrey, G., Berg-Lyons, D., et al. Cohabiting family members share microbiota with one another and with their dogs. Elife, 2, 2013, e00458.
14. [14] Stahringer, S.S., Clemente, J.C., Corley, R.P., Hewitt, J., Knights, D., Walters, W.A., et al. Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood. Genome Res 22:11 (2012), 2146–2152.
15. [15] Wen A, Weyant R, McNeil D, Crout R, Marazita M, Foxman B. Family-level education and smoking habits affect sibling's dental caries. (Submitted).
16. [16] Polk, D.E., Weyant, R.J., Crout, R.J., McNeil, D.W., Tarter, R.E., Thomas, J.G., et al. Study protocol of the Center for Oral Health Research in Appalachia (COHRA) etiology study. BMC Oral Health, 8, 2008, 18.
17. [17] Gloor, G.B., Hummelen, R., Macklaim, J.M., Dickson, R.J., Fernandes, A.D., MacPhee, R., et al. Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products. PLoS One, 5(10), 2010, e15406.
18. [18] Magoč, T., Salzberg, S.L., FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:21 (2011), 2957–2963.
19. [19] Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:5 (2010), 335–336.
20. [20] Griffen, A.L., Beall, C.J., Firestone, N.D., Gross, E.L., Difranco, J.M., Hardman, J.H., et al. CORE: a phylogenetically-curated 16S rDNA database of the core oral microbiome. PLoS One, 6(4), 2011, e19051.
21. [21] Wang, Q., Garrity, G.M., Tiedje, J.M., Cole, J.R., Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:16 (2007), 5261–5267.
22. [22] Caporaso, J.G., Bittinger, K., Bushman, F.D., DeSantis, T.Z., Andersen, G.L., Knight, R., PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:2 (2010), 266–267.
23. [23] Ling, Z., Kong, J., Jia, P., Wei, C., Wang, Y., Pan, Z., et al. Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing. Microb Ecol 60:3 (2010), 677–690.
24. [24] Gomar-Vercher, S., Cabrera-Rubio, R., Mira, A., Montiel-Company, J.M., Almerich-Silla, J.M., Relationship of children's salivary microbiota with their caries status: a pyrosequencing study. Clin Oral Investig 18:9 (2014), 2087–2094.
25. [25] Jiang, W., Ling, Z., Lin, X., Chen, Y., Zhang, J., Yu, J., et al. Pyrosequencing analysis of oral microbiota shifting in various caries states in childhood. Microb Ecol 67:4 (2014), 962–969.
26. [26] Lif Holgerson, P., Öhman, C., Rönnlund, A., Johansson, I., Maturation of oral microbiota in children with or without dental caries. PLoS One, 10(5), 2015, e0128534.
27. [27] Crielaard, W., Zaura, E., Schuller, A.A., Huse, S.M., Montijn, R.C., Keijser, B.J.F., Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health. BMC Med Genomics, 4, 2011, 22.
28. [28] Aas, J.A., Griffen, A.L., Dardis, S.R., Lee, A.M., Olsen, I., Dewhirst, F.E., et al. Bacteria of dental caries in primary and permanent teeth in children and young adults. J Clin Microbiol 46:4 (2008), 1407–1417.
29. [29] Ling, Z., Liu, X., Wang, Y., Li, L., Xiang, C., Pyrosequencing analysis of the salivary microbiota of healthy Chinese children and adults. Microb Ecol 65:2 (2013), 487–495.
30. [30] Kanasi, E., Dewhirst, F.E., Chalmers, N.I., Kent, R. Jr., Moore, A., Hughes, C.V., et al. Clonal analysis of the microbiota of severe early childhood caries. Caries Res 44:5 (2010), 485–497.
31. [31] Jiang, W., Zhang, J., Chen, H., Pyrosequencing analysis of oral microbiota in children with severe early childhood dental caries. Curr Microbiol 67:5 (2013), 537–542.
32. [32] Foxman, B., Srinivasan, U., Wen, A., Zhang, L., Marrs, C.F., Goldberg, D., et al. Exploring the effect of dentition, dental decay and familiality on oral health using metabolomics. Infect Genet Evol 22 (2014), 201–207.