Chapter 33
Microbiome Diversity in Human Saliva
Ivan Nasidze,
Mark Stoneking,
Ivan Nasidze
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
Search for more papers by this authorMark Stoneking
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
Search for more papers by this authorIvan Nasidze,
Mark Stoneking,
Ivan Nasidze
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
Search for more papers by this authorMark Stoneking
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
Search for more papers by this authorBook Editor(s):Frans J. de Bruijn,
Frans J. de Bruijn
Laboratory of Plant Micro-organism Interaction, CNRS-INRA, Castanet Tolosan, France
Search for more papers by this authorFirst published: 16 September 2011
Summary
This chapter contains sections titled:
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Introduction
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Results and Discussion
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References
REFERENCES
- Aas J, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. 2005. Defining the normal bacterial flora of the oral cavity. J. Clin. Microbiol. 43: 5721–5732.
- Andersson AF, Lindberg M, Jakobsson H, Bäckhed F, Nyrén P, Engstrand L. 2008. Comparative Analysis of Human Gut Micro-biota by Barcoded Pyrosequencing. PLoS ONE 3(7): e2836.
- Becker MR, Paster BJ, Leys EJ, Moeschberger ML, Kenyon SG, et al. 2002. Molecular analysis of bacterial species associated with childhood caries. J. Clin. Microbiol. 40: 1001–1009.
- Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, et al., 2007. The ribosomal database project (RDP-II): Introducing myRDP space and quality controlled public data. Nucleic Acids Res. 35: D169–D172.
- Corby PM, Bretz WA, Hart TC, Schork NJ, Wessel J, Lyons-Weiler J, Paster BJ. 2007. Heritability of oral microbial species in caries-active and caries-free twins. Twin Res. Hum. Genet. 10: 821–828.
- Dethlefsen L, McFall-Ngai M, Relman DA. 2007. An ecological and evolutionary perspective on human–microbe mutualism and disease. Nature 449: 811–818.
- Diaz PI, Chalmers NI, Rickard AH, Kong C, Milburn CL, Palmer RJ, Kolenbrander PE. 2006. Molecular characterization of subject-specific oral microflora during initial colonization of enamel. Appl. Environ. Microbiol. 72: 2837–2848.
- Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al., 2005. Diversity of the human intestinal microbial flora. Science 308: 1635–1638.
- Fabian TK, Fejerdy P, Csermely P. 2008. Salivary genomics, transcriptomics, and proteomics: The emerging concept of the oral ecosystem and their use in the early diagnosis of cancer and other diseases. Curr. Genomics 9: 11–21.
- Falush D, Wirth T, Linz B, Pritchard JK, Stephens M, et al., 2003. Traces of human migrations in Helicobacter pylori populations. Science 299: 1582–1585.
- Faveri M, Mayer MPA, Feres M, de Figueiredo LC, Dewhirst FE, Paster BJ. 2008. Microbiological diversity of generalized aggressive periodontitis by 16S rRNA clonal analysis. Oral Microbiol. Immunol. 23: 112–118.
- Grice EA, Kong HH, Renaud G, Young AC, Bouffard GG, et al. 2008. A diversity profile of the human skin microbiota. Genome Res. 18: 1043–1050.
- Hansen TV, Simonsen MK, Nielsen FC, Hundrup YA. 2007. Collection of blood, saliva, and buccal cell samples in a pilot study on the Danish nurse cohort: Comparison of the response rate and quality of genomic DNA. Cancer Epidemiol. Biomarkers Prev. 16: 2072–2076.
- Keijser BJF, Zaura E, Huse SM, van der Vossen JMBM, Schuren FHJ, Montijn RC, ten Cate JM, Crielaard W. 2008. Pyrosequencing analysis of the oral microflora of healthy adults. J. Dental Res. 87: 1016–1020.
- Kang JG, Kim SH, Ahn TY. 2006. Bacterial diversity in the human saliva from different ages. J. Microbiol. 44: 572–576.
- Kilian M, Frandsen EVG, Haubek H, Poulsen K. 2006. The etiology of periodontal disease revisited by population genetic analysis. Periodontol. 2000 42: 158–179.
- Kumar PS, Griffen AL, Barton JA, Paster BJ, Moeschberger ML, Leys EJ. 2003. New bacterial species associated with chronic periodontitis. J. Dent. Res. 82: 338–344.
- Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, et al., 2009. Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J. Microbiol. Methods 3(5): e130.
- Lerat E, Daubin V, Ochman H, Moran NA. 2005. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 3: e130.
- Li Y, Ismail AI, Ge Y, Tellez M, Sohn W. 2007. Similarity of bacterial populations in saliva from African-American mother–child dyads. J. Clin. Microbiol. 45: 3082–3085.
- Linz B, Balloux F, Moodley Y, Manica A, Liu H, et al., 2007. An African origin for the intimate association between humans and Helicobacter pylori. Nature 445: 915–918.
- Liu Z, DeSantis TZ, Andersen GL, Knight R. 2008. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. 36: e120.
- Machado de Oliveira JC, Siqueira JF, Rocas IN, Baumgartner JC, Xia T, Peixoto RS, Rosado AS. 2007. Bacterial community profiles of endodontic abscesses from Brazilian and USA subjects as compared by denaturing gradient gel electrophoresis analysis. Oral Microbiol. Immunol. 22: 14–18.
- Mullard A. 2008. Microbiology: The inside story. Nature 453: 578–580.
- Nasidze I, Li J, Quinque D, Tang, K, Stoneking M. 2009a. Global Diversity in the Human Salivary Microbiome. Genom. Res. 19: 636–643.
- Nasidze I, Quinque D, Li J, Li M, Tang K, Stoneking M. 2009b. Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches. Anal. Biochem. 391: 64–68.
- Oakley BB, Fiedler TL, Marrazzo JM, Fredricks DN. 2008. The diversity of human vaginal bacterial communities and their association with clinically defined bacterial vaginosis. Appl. Environ. Micro-biol. 74: 4898–4909.
- Paster BJ, Olsen I, Aas J, Dewhirst FE. 2006. The breadth of bacterial diversity in the human periodontal pocket and other oral sites. Periodontol. 2000 42: 80–87.
- Quinque D, Kittler R, Kayser M, Stoneking M, Nasidze I. 2006. Evaluation of saliva as a source of human DNA for population and association studies. Anal. Biochem. 353: 272–277.
- Schipper RG, Silletti E, Vingerhoeds MH. 2007. Saliva as research material: Biochemical, physicochemical and practical aspects. Arch. Oral. Biol. 52: 1114–1135.
- Sundquist A, Bigdeli S, Jalili R, Druzin ML, Waller S, Pullen KM, et al., 2007. Bacterial flora typing with deep, targeted, chip-based pyrosequencing. BMC Microbiol. 7: 108.
- Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. 2007. The human microbiome project. Nature 449: 804–810.
- Wirth T, Wang X, Linz B, Novick RP, Lum JK, Blaser M, Morelli G, Falush D, Achtman M. 2004. Distinguishing human ethnic groups by means of sequences from Helicobacter pylori: Lessons from Ladakh. Proc. Natl. Acad. Sci. USA 101: 4746–4751.