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. 2010 Aug;4(8):962-74.
doi: 10.1038/ismej.2010.30. Epub 2010 Mar 25.

Bacterial diversity in the oral cavity of 10 healthy individuals

Elisabeth M Bik  1 , Clara Davis Long, Gary C Armitage, Peter Loomer, Joanne Emerson, Emmanuel F Mongodin, Karen E Nelson, Steven R Gill, Claire M Fraser-Liggett, David A Relman
Affiliations

Bacterial diversity in the oral cavity of 10 healthy individuals

Elisabeth M Bik et al. ISME J. 2010 Aug.

Abstract

The composition of the oral microbiota from 10 individuals with healthy oral tissues was determined using culture-independent techniques. From each individual, 26 specimens, each from different oral sites at a single point in time, were collected and pooled. An 11th pool was constructed using portions of the subgingival specimens from all 10 individuals. The 16S ribosomal RNA gene was amplified using broad-range bacterial primers, and clone libraries from the individual and subgingival pools were constructed. From a total of 11,368 high-quality, nonchimeric, near full-length sequences, 247 species-level phylotypes (using a 99% sequence identity threshold) and 9 bacterial phyla were identified. At least 15 bacterial genera were conserved among all 10 individuals, with significant interindividual differences at the species and strain level. Comparisons of these oral bacterial sequences with near full-length sequences found previously in the large intestines and feces of other healthy individuals suggest that the mouth and intestinal tract harbor distinct sets of bacteria. Co-occurrence analysis showed significant segregation of taxa when community membership was examined at the level of genus, but not at the level of species, suggesting that ecologically significant, competitive interactions are more apparent at a broader taxonomic level than species. This study is one of the more comprehensive, high-resolution analyses of bacterial diversity within the healthy human mouth to date, and highlights the value of tools from macroecology for enhancing our understanding of bacterial ecology in human health.

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Figures

Figure 1
Figure 1. Relative abundance of phylum members of the oral communities from 10 healthy individuals
A total of 11 368 bacterial rRNA gene sequences derived from pools of specimens from different oral habitats, from each of 10 healthy individuals (numbered 1 to 10), as well as from a pool of all subgingival samples (S), was analyzed and assigned to phyla (color-coded, according to the scheme at the right). “Total” refers to the combined set of sequences from all pools. The number of clones in each rRNA gene library is given below the name of the pool.
Figure 2
Figure 2. Phylogenetic relationships and relative abundance of the genera found in pools of oral specimens
A. Phylogenetic tree for the 247 OTUs found in this study, grouped by genus. A 95% sequence similarity threshold was used for unclassified groups. The tree was constructed by neighbor-joining analysis with an Olsen correction. Bootstrap values >=50 (expressed as percentages of 1000 replicates) are shown at branch points. The scale bar represents evolutionary distance (10 substitutions per 100 nucleotides). B. Relative abundance of genera in each of the 11 oral specimens pools displayed with gray scale values (white, 0% present; black, 100% of clone library; exact scale shown at the bottom). 1–10, each of the individual subject pools; S, subgingival, T, total. Genera are shown in the same order as in A.
Figure 3
Figure 3. Variation in patterns of diversity
Unifrac Principal Components Analysis (PCA) was performed using weighted, normalized abundance data (Lozupone 2006). A. Analysis of oral specimen pools from each of 10 healthy subjects (white circles, females, n=5; grey circles, males, n=5), and 1 pool of the subgingival specimens from all of these 10 subjects (black circle). B. Analysis of the oral specimen pool data from this study (white circles, n=11), data from additional oral specimen pools extracted with a different DNA extraction method (grey circles, n=3, unpublished data), and previously-published data from human colon samples (grey squares, n=18, Eckburg et al. 2005) and human stool samples (grey triangles, n=3, Eckburg et al. 2005; black triangles, n=15, Dethlefsen et al. 2008). All sequences were compared using the same alignment and 1253-nucleotide filter.
Figure 4
Figure 4. Checkerboard (C−) scores for each possible combination of two genera
The C-scores are shown in gray scale. White depicts a C-score of 0 for genera always found together. Darker colors show higher C-scores for genera that co-occur less frequently than expected. The highest C-score in this dataset, 16, was found for the Abiotrophia-Treponema genus pair, two fairly abundant genera never found together. Genera are ordered according to their overall abundance in the 10 individual mouth pools. The numbers after the genus names indicate the number of individuals (out of 10) in which that genus was found. The 16 taxa that were found in all 10 individuals, as expected, all show a C-score of 0 (white). Data from the subgingival pool were not included in this analysis.
Figure 5
Figure 5. Schematic depiction of oral community membership among ten healthy individuals
Inner circle, bacterial genera found in all 10 individuals (100%); second circle, present in 6 to 9 out of 10 individuals (51–99%); third circle, present in 3 to 5 individuals (21–50%); outer circle, present in 1 to 2 individuals (1–20%). Genera are grouped per phylum.
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References

    1. Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol. 2005;43:5721–32. - PMC - PubMed
    1. Chao A, Chazdon RL, Colwell RK, Shen T-J. A new statistical approach for assessing compositional similarity based on incidence and abundance data. Ecology Letters. 2005;8:148–159.
    1. Cogen AL, Nizet V, Gallo RL. Skin microbiota: a source of disease or defence? Br J Dermatol. 2008;158:442–55. - PMC - PubMed
    1. Colwell RK. EstimateS: Statistical estimation of species richness and shared species from specimens. Version 7. 2005. User’s Guide and application published at: http://purl.oclc.org/estimates)
    1. 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 - PMC - PubMed

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