1887

Abstract

The oral microbiota plays an important role in buccal health and in diseases such as periodontitis and meningitis. The study of the human oral bacteria has so far focused on subjects from Western societies, while little is known about subjects from isolated communities. This work determined the composition of the oral mucosa microbiota from six Amazon Amerindians, and tested a sample preservation alternative to freezing. Paired oral swabs were taken from six adults of Guahibo ethnicity living in the community of Platanillal, Amazonas State, Venezuela. Replicate swabs were preserved in liquid nitrogen and in Aware Messenger fluid (Calypte). Buccal DNA was extracted, and the V2 region of the 16S rRNA gene was amplified and pyrosequenced. A total of 17 214 oral bacterial sequences were obtained from the six subjects; these were binned into 1034 OTUs from 10 phyla, 30 families and 51 genera. The oral mucosa was highly dominated by four phyla: (mostly the genera and ), (mostly ), () and (). Although the microbiota were similar at the phylum level, the Amerindians shared only 62 % of the families and 23 % of the genera with non-Amerindians from previous studies, and had a lower richness of genera (51 vs 177 reported in non-Amerindians). The Amerindians carried unidentified members of the phyla , and and their microbiota included soil bacteria Gp1 () and (), and the rare genus (). Preserving buccal swabs in the Aware Messenger oral fluid collection device substantially altered the bacterial composition in comparison to freezing, and therefore this method cannot be used to preserve samples for the study of microbial communities.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.043174-0
2010-11-01
2020-03-31
Loading full text...

Full text loading...

/deliver/fulltext/micro/156/11/3282.html?itemId=/content/journal/micro/10.1099/mic.0.043174-0&mimeType=html&fmt=ahah

References

  1. Ausec L., Kraighera B., Mandic-Mulec I.. 2009; Differences in the activity and bacterial community structure of drained grassland and forest peat soils. Soil Biol Biochem41:1874–1881
    [Google Scholar]
  2. Bik E. M., Eckburg P. B., Gill S. R., Nelson K. E., Purdom E. A., Francois F., Perez-Perez G., Blaser M. J., Relman D. A.. 2006; Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci U S A103:732–737
    [Google Scholar]
  3. Bik E. M., Long C. D., Armitage G. C., Loomer P., Emerson J., Mongodin E. F., Nelson K. E., Gill S. R., Fraser-Liggett C. M., Relman D. A.. 2010; Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J4:962–974
    [Google Scholar]
  4. Brambilla E., Strohmenger L., Vogel G.. 1992; The effect of storage in liquid nitrogen on the isolation of oral yeasts in human saliva. Arch Oral Biol37:237–239
    [Google Scholar]
  5. Castro H. F., Classen A. T., Austin E. E., Norby R. J., Schadt C. W.. 2010; Soil microbial community responses to multiple experimental climate change drivers. Appl Environ Microbiol76:999–1007
    [Google Scholar]
  6. DeSantis T. Z. Jr, Hugenholtz P., Keller K., Brodie E. L., Larsen N., Piceno Y. M., Phan R., Andersen G. L.. 2006a; NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res34:W394–W399
    [Google Scholar]
  7. DeSantis T. Z., Hugenholtz P., Larsen N., Rojas M., Brodie E. L., Keller K., Huber T., Dalevi D., Hu P., Andersen G. L.. 2006b; Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol72:5069–5072
    [Google Scholar]
  8. Domínguez-Bello M. G., Costello E. K., Contreras M., Magris M., Hidalgo G., Fierer N., Knight R.. 2010; Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A107:11971–11975
    [Google Scholar]
  9. Engelbrektson A., Kunin V., Wrighton K. C., Zvenigorodsky N., Chen F., Ochman H., Hugenholtz P.. 2010; Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J4:642–647
    [Google Scholar]
  10. Fierer N., Hamady M., Lauber C. L., Knight R.. 2008; The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A105:17994–17999
    [Google Scholar]
  11. Foster G., Ross H. M., Malnick H., Willems A., Hutson R. A., Reid R. J., Collins M. D.. 2000; Phocoenobacter uteri gen. nov., sp. nov., a new member of the family Pasteurellaceae Pohl (1979) 1981 isolated from a harbour porpoise ( Phocoena phocoena. Int J Syst Evol Microbiol50:135–139
    [Google Scholar]
  12. Grice E. A., Kong H. H., Conlan S., Deming C. B., Davis J., Young A.C., NISC Comparative Sequencing Program Bouffard G. G., Blakesley R. W.. other authors 2009; Topographical and temporal diversity of the human skin microbiome. Science324:1190–1192
    [Google Scholar]
  13. Hamady M., Walker J. J., Harris J. K., Gold N. J., Knight R.. 2008; Error-correcting barcoded primers allow hundreds of samples to be pyrosequenced in multiplex. Nat Methods5:235–237
    [Google Scholar]
  14. Huyghe A., Francois P., Charbonnier Y., Tangomo-Bento M., Bonetti E. J., Paster B. J., Bolivar I., Baratti-Mayer D., Pittet D.. 2008; Novel microarray design strategy to study complex bacterial communities. Appl Environ Microbiol74:1876–1885
    [Google Scholar]
  15. Keijser B. J., Zaura E., Huse S. M., van der Vossen J. M., Schuren F. H., Montijn R. C., ten Cate J. M., Crielaard W.. 2008; Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res87:1016–1020
    [Google Scholar]
  16. Kroes I., Lepp P. W., Relman D. A.. 1999; Bacterial diversity within the human subgingival crevice. Proc Natl Acad Sci U S A96:14547–14552
    [Google Scholar]
  17. Lazarevic V., Whiteson K., Huse S., Hernandez D., Farinelli L., Osterås M., Schrenzel J., François P.. 2009; Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Methods79:266–271
    [Google Scholar]
  18. Li W. Z., Godzik A.. 2006; Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics22:1658–1659
    [Google Scholar]
  19. Lozupone C., Knight R.. 2005; UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol71:8228–8235
    [Google Scholar]
  20. Lozupone C. A., Hamady M., Kelley S. T., Knight R.. 2007; Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol73:1576–1585
    [Google Scholar]
  21. Meyer M., Stenzel U., Hofreiter M.. 2008; Parallel tagged sequencing on the 454 platform. Nat Protoc3:267–278
    [Google Scholar]
  22. Nasidze I., Li J., Quinque D., Tang K., Stoneking M.. 2009a; Global diversity in the human salivary microbiome. Genome Res19:636–643
    [Google Scholar]
  23. 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 Biochem391:64–68
    [Google Scholar]
  24. Paster B. J., Boches S. K., Galvin J. L., Ericson R. E., Lau C. N., Levanos V. A., Sahasrabudhe A., Dewhirst F. E.. 2001; Bacterial diversity in human subgingival plaque. J Bacteriol183:3770–3783
    [Google Scholar]
  25. Ravel J., Gajer P., Abdo Z., Schneider G. M., Koenig S. S., McCulle S. L., Karlebach S., Gorle R., Russell J.. other authors (2010; Microbes and Health Sackler Colloquium: vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A Aug 19 [Epub ahead of print]
    [Google Scholar]
  26. Sheneman L., Evans J., Foster J. A.. 2006; Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics22:2823–2824
    [Google Scholar]
  27. Ueki A., Akasaka H., Suzuki D., Hattori S., Ueki K.. 2006; Xylanibacter oryzae gen. nov., sp. nov., a novel strictly anaerobic, Gram-negative, xylanolytic bacterium isolated from rice-plant residue in flooded rice-field soil in Japan. Int J Syst Evol Microbiol562215–2221
    [Google Scholar]
  28. Wang Q., Garrity G. M., Tiedje J. M., Cole J. R.. 2007; Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol73:5261–5267
    [Google Scholar]
  29. Zaura E., Keijser B. J., Huse S. M., Crielaard W.. 2009; Defining the healthy “core microbiome” of oral microbial communities. BMC Microbiol9:259
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.043174-0
Loading
/content/journal/micro/10.1099/mic.0.043174-0
Loading

Data & Media loading...

Most cited this month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error